diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/SpeciesSbmlParser.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/SpeciesSbmlParser.java
index f2d32631948e78f156bd19f4a6230a7e527da0cb..14d80344012c7e2ba363496b5494833e79647283 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/SpeciesSbmlParser.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/SpeciesSbmlParser.java
@@ -26,6 +26,7 @@ import lcsb.mapviewer.converter.model.celldesigner.structure.fields.CellDesigner
import lcsb.mapviewer.converter.model.celldesigner.structure.fields.SpeciesState;
import lcsb.mapviewer.model.map.compartment.Compartment;
import lcsb.mapviewer.model.map.compartment.PathwayCompartment;
+import lcsb.mapviewer.model.map.kinetics.SbmlUnitType;
import lcsb.mapviewer.model.map.model.ModelData;
import lcsb.mapviewer.model.map.species.AntisenseRna;
import lcsb.mapviewer.model.map.species.Gene;
@@ -44,582 +45,598 @@ import lcsb.mapviewer.model.map.species.field.PositionToCompartment;
*/
public class SpeciesSbmlParser extends AbstractElementXmlParser<CellDesignerSpecies<?>, Species> {
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private Logger logger = Logger.getLogger(SpeciesSbmlParser.class.getName());
-
- /**
- * Collection of {@link CellDesignerElement cell designer elements} parsed
- * from xml.
- */
- private CellDesignerElementCollection elements;
-
- /**
- * Default constructor. Model is required because some nodes require access to
- * other parts of the model.
- *
- * @param elements
- * collection of {@link CellDesignerElement cell designer elements}
- * parsed from xml
- */
- public SpeciesSbmlParser(CellDesignerElementCollection elements) {
- this.elements = elements;
- }
-
- @Override
- public Pair<String, CellDesignerSpecies<?>> parseXmlElement(Node spieciesNode) throws InvalidXmlSchemaException {
-
- NodeList list = spieciesNode.getChildNodes();
-
- Node annotationNode = null;
- Node notesNode = null;
- for (int i = 0; i < list.getLength(); i++) {
- Node node = list.item(i);
- if (node.getNodeType() == Node.ELEMENT_NODE) {
- if (node.getNodeName().equals("annotation")) {
- annotationNode = node;
- } else if (node.getNodeName().equals("notes")) {
- notesNode = node;
- } else {
- throw new InvalidXmlSchemaException("Unknown element of annotation " + node.getNodeName());
- }
- }
- }
-
- if (annotationNode == null) {
- throw new InvalidXmlSchemaException("No annotation node in SBML/model/listOfSpecies/species");
- }
-
- list = annotationNode.getChildNodes();
- Node extensionNode = null;
- Node rdfNode = null;
-
- for (int i = 0; i < list.getLength(); i++) {
- Node node = list.item(i);
- if (node.getNodeType() == Node.ELEMENT_NODE) {
- if (node.getNodeName().equals("celldesigner:extension")) {
- extensionNode = node;
- } else if (node.getNodeName().equals("rdf:RDF")) {
- rdfNode = node;
- } else {
- throw new InvalidXmlSchemaException("Unknown element of annotation " + node.getNodeName());
- }
- }
- }
-
- if (extensionNode == null) {
- throw new InvalidXmlSchemaException("No celldesigner:extension node in SBML/model/listOfSpecies/species/annotation");
- }
-
- list = extensionNode.getChildNodes();
- Node speciesIdentity = null;
- Node positionToCompartment = null;
- for (int i = 0; i < list.getLength(); i++) {
- Node node = list.item(i);
- if (node.getNodeType() == Node.ELEMENT_NODE) {
- if (node.getNodeName().equals("celldesigner:speciesIdentity")) {
- speciesIdentity = node;
- } else if (node.getNodeName().equals("celldesigner:positionToCompartment")) {
- positionToCompartment = node;
- } else if (node.getNodeName().equals("celldesigner:listOfCatalyzedReactions")) {
- // we can ignore it - every node on the map contains information about
- // itself
- continue;
- } else {
- throw new InvalidXmlSchemaException("[" + getNodeAttr("id", spieciesNode) + "]\tUnknown element of celldesigner:extension " + node.getNodeName());
- }
- }
- }
-
- if (speciesIdentity == null) {
- throw new InvalidXmlSchemaException("No celldesigner:speciesIdentity node in SBML/model/listOfSpecies/species/annotation/extension");
- }
-
- Pair<String, CellDesignerSpecies<?>> result = parseSpeciesIdentity(speciesIdentity);
-
- CellDesignerSpecies<?> species = result.getRight();
- if (positionToCompartment != null) {
- PositionToCompartment position = PositionToCompartment.getByString(getNodeValue(positionToCompartment));
- if (position == null) {
- throw new InvalidXmlSchemaException("Unknown position on compartment: " + getNodeValue(positionToCompartment));
- }
- species.setPositionToCompartment(position);
- }
-
- // we ignore metaid - it's useless and obstruct data model
- // species.setMetaId(getNodeAttr("metaid", spieciesNode));
- species.setElementId(getNodeAttr("id", spieciesNode));
- species.setName(decodeName(getNodeAttr("name", spieciesNode)));
- species.setInitialAmount(getNodeAttr("initialAmount", spieciesNode));
- species.setInitialConcentration(getNodeAttr("initialConcentration", spieciesNode));
- species.setCharge(getNodeAttr("charge", spieciesNode));
- species.setOnlySubstanceUnits(getNodeAttr("hasOnlySubstanceUnits", spieciesNode));
-
- CellDesignerCompartment compartment = elements.getElementByElementId(getNodeAttr("compartment", spieciesNode));
- if (compartment != null) {
- species.setParent(compartment);
- }
-
- if (notesNode != null) {
- species.setNotes(getRap().getNotes(notesNode));
- }
-
- if (rdfNode != null) {
- XmlAnnotationParser xmlAnnotationParser = new XmlAnnotationParser();
- species.addMiriamData(xmlAnnotationParser.parseRdfNode(annotationNode.getChildNodes()));
- }
-
- return result;
- }
-
- @Override
- public String toXml(Species species) {
- StringBuilder builder = new StringBuilder();
- StringBuilder attributesBuilder = new StringBuilder();
- attributesBuilder.append(" name=\"" + escapeXml(encodeName(species.getName())) + "\"");
- attributesBuilder.append(" id=\"" + elements.getElementId(species) + "\"");
- attributesBuilder.append(" metaid=\"" + elements.getElementId(species) + "\"");
- if (species.getInitialAmount() != null) {
- attributesBuilder.append(" initialAmount=\"" + species.getInitialAmount() + "\"");
- }
- if (species.getInitialConcentration() != null) {
- attributesBuilder.append(" initialConcentration=\"" + species.getInitialConcentration() + "\"");
- }
- if (species.getCharge() != null) {
- attributesBuilder.append(" charge=\"" + species.getCharge() + "\"");
- }
- if (species.hasOnlySubstanceUnits() != null) {
- attributesBuilder.append(" hasOnlySubstanceUnits=\"" + species.hasOnlySubstanceUnits() + "\"");
- }
-
- Compartment comp = null;
- // we have to exclude artifitial compartment aliases, becuase they aren't
- // exported to CellDesigner file
- if (species.getCompartment() != null && !(species.getCompartment() instanceof PathwayCompartment)) {
- comp = species.getCompartment();
- } else if (species.getComplex() == null) {
- ModelData modelData = species.getModelData();
- if (modelData != null) {
- for (Compartment cAlias : modelData.getModel().getCompartments()) {
- if (!(cAlias instanceof PathwayCompartment) && cAlias.cross(species)) {
- if (comp == null) {
- comp = cAlias;
- } else if (comp.getSize() > cAlias.getSize()) {
- comp = cAlias;
- }
- }
- }
- }
- }
-
- if (comp != null) {
- attributesBuilder.append(" compartment=\"" + elements.getElementId(comp) + "\"");
- } else {
- attributesBuilder.append(" compartment=\"default\"");
- }
- builder.append("<species " + attributesBuilder.toString() + ">");
-
- if ((species.getNotes() != null && !species.getNotes().equals("")) || species.getSymbol() != null || species.getFullName() != null
- || species.getSynonyms().size() > 0) {
- builder.append("<notes>");
- builder.append("<html xmlns=\"http://www.w3.org/1999/xhtml\"><head><title/></head><body>");
- RestAnnotationParser rap = new RestAnnotationParser();
- builder.append(rap.createAnnotationString(species));
- if (species.getNotes() != null) {
- builder.append(species.getNotes());
- }
- builder.append("</body></html>");
- builder.append("</notes>\n");
- }
- builder.append("<annotation>");
- builder.append("<celldesigner:extension>");
- if (species.getPositionToCompartment() != null) {
- builder.append("<celldesigner:positionToCompartment>" + species.getPositionToCompartment().getStringName() + "</celldesigner:positionToCompartment>");
- }
- builder.append(speciesIdentityToXml(species));
-
- builder.append("</celldesigner:extension>\n");
-
- XmlAnnotationParser xmlAnnotationParser = new XmlAnnotationParser();
- builder.append(xmlAnnotationParser.dataSetToXmlString(species.getMiriamData()));
-
- builder.append("</annotation>\n");
-
- builder.append("</species>\n");
- return builder.toString();
- }
-
- /**
- * Creates speciesIdentity xml node for the {@link CellDesignerSpecies}.
- *
- * @param species
- * species to be transformed into xml
- * @return speciesIdentity xml node
- */
- String speciesIdentityToXml(Species species) {
- StringBuilder sb = new StringBuilder();
- String classType = "";
- SpeciesMapping mapping = SpeciesMapping.getMappingByModelClass(species.getClass());
- if (mapping != null) {
- classType = mapping.getCellDesignerString();
- } else {
- throw new InvalidArgumentException("Invalid species class type: " + species.getClass().getName());
- }
- sb.append("<celldesigner:speciesIdentity>");
- sb.append("<celldesigner:class>" + classType + "</celldesigner:class>\n");
- if (species instanceof Rna) {
- sb.append("<celldesigner:rnaReference>r_" + elements.getElementId(species) + "</celldesigner:rnaReference>\n");
- } else if (species instanceof Protein) {
- sb.append("<celldesigner:proteinReference>p_" + elements.getElementId(species) + "</celldesigner:proteinReference>\n");
- } else if (species instanceof Gene) {
- sb.append("<celldesigner:geneReference>g_" + elements.getElementId(species) + "</celldesigner:geneReference>\n");
- } else if (species instanceof AntisenseRna) {
- sb.append("<celldesigner:antisensernaReference>ar_" + elements.getElementId(species) + "</celldesigner:antisensernaReference>\n");
- }
- SpeciesState state = new SpeciesState(species);
- sb.append(speciesStateToXml(state));
- sb.append("<celldesigner:name>" + escapeXml(encodeName(species.getName())) + "</celldesigner:name>\n");
-
- Boolean hypothetical = species.getHypothetical();
- if (hypothetical != null) {
- sb.append("<celldesigner:hypothetical>" + hypothetical + "</celldesigner:hypothetical>\n");
- }
-
- sb.append("</celldesigner:speciesIdentity>\n");
- return sb.toString();
- }
-
- /**
- * Creates CellDesigner species state into xml node.
- *
- * @param state
- * state of the species.
- * @return CellDesigner xml node used for description of the state
- */
- String speciesStateToXml(SpeciesState state) {
- StringBuilder sb = new StringBuilder();
- if (state.getHomodimer() != 1) {
- sb.append("<celldesigner:homodimer>" + state.getHomodimer() + "</celldesigner:homodimer>\n");
- }
- if (state.getStructuralState() != null && !state.getStructuralState().equals("")) {
- sb.append("<celldesigner:listOfStructuralStates>\n");
- sb.append(
- "<celldesigner:structuralState structuralState=\"" + state.getStructuralState() + "\">" + state.getStructuralState()
- + "</celldesigner:structuralState>");
- sb.append("</celldesigner:listOfStructuralStates>\n");
- }
- if (state.getModifications().size() > 0) {
- sb.append("<celldesigner:listOfModifications>\n");
- for (CellDesignerModificationResidue mr : state.getModifications()) {
- sb.append(modificationResidueToXml(mr));
- }
- sb.append("</celldesigner:listOfModifications>\n");
- }
- if (sb.length() > 0) {
- sb.insert(0, "<celldesigner:state>\n");
- sb.append("</celldesigner:state>\n");
- }
- return sb.toString();
- }
-
- /**
- * Parses CellDesigner SpeciesIdentity node into {@link CellDesignerSpecies}.
- *
- * @param rootNode
- * xml node to parse
- * @return {@link Pair} of Species retrieved from SpeciesIdentity node and
- * CellDesigner identifier
- * @throws InvalidXmlSchemaException
- * thrown when there is a problem with xml
- */
- public Pair<String, CellDesignerSpecies<?>> parseSpeciesIdentity(Node rootNode) throws InvalidXmlSchemaException {
- NodeList nodes = rootNode.getChildNodes();
- CellDesignerSpecies<?> result = new CellDesignerSpecies<Species>();
- Node classNode = getNode("celldesigner:class", nodes);
- if (classNode == null) {
- throw new InvalidXmlSchemaException("Species node in Sbml model doesn't contain node \"celldesigner:class\".");
- } else {
- String value = getNodeValue(classNode);
- SpeciesMapping mapping = SpeciesMapping.getMappingByString(value);
- if (mapping != null) {
- result = mapping.createSpecies(result);
- } else {
- throw new InvalidXmlSchemaException("Species node in Sbml model is of unknown type: " + value);
- }
- }
- String identifier = "";
- for (int x = 0; x < nodes.getLength(); x++) {
- Node node = nodes.item(x);
- if (node.getNodeType() == Node.ELEMENT_NODE) {
- if (node.getNodeName().equalsIgnoreCase("celldesigner:class")) {
- continue;
- } else if (node.getNodeName().equalsIgnoreCase("celldesigner:proteinReference")) {
- if (result instanceof CellDesignerProtein) {
- identifier = getNodeValue(node);
- } else {
- throw new InvalidXmlSchemaException("Wrong class type for protein reference: " + result.getClass().getName());
- }
- } else if (node.getNodeName().equalsIgnoreCase("celldesigner:geneReference")) {
- if (result instanceof CellDesignerGene) {
- identifier = getNodeValue(node);
- } else {
- throw new InvalidXmlSchemaException("Wrong class type for gene reference: " + result.getClass().getName());
- }
- } else if (node.getNodeName().equalsIgnoreCase("celldesigner:rnaReference")) {
- if (result instanceof CellDesignerRna) {
- identifier = getNodeValue(node);
- } else {
- throw new InvalidXmlSchemaException("Wrong class type for rna reference: " + result.getClass().getName());
- }
- } else if (node.getNodeName().equalsIgnoreCase("celldesigner:antisensernaReference")) {
- if (result instanceof CellDesignerAntisenseRna) {
- identifier = getNodeValue(node);
- } else {
- throw new InvalidXmlSchemaException("Wrong class type for antisense rna reference: " + result.getClass().getName());
- }
- } else if (node.getNodeName().equalsIgnoreCase("celldesigner:hypothetical")) {
- result.setHypothetical(getNodeValue(node));
- } else if (node.getNodeName().equalsIgnoreCase("celldesigner:name")) {
- result.setName(decodeName(getNodeValue(node)));
- } else if (node.getNodeName().equalsIgnoreCase("celldesigner:state")) {
- SpeciesState state = parseXmlSpeciesState(node);
- processStateDataInSpecies(result, state);
- } else {
- throw new InvalidXmlSchemaException("Unknown element of celldesigner:speciesIdentity: " + node.getNodeName());
- }
- }
-
- }
- return new Pair<String, CellDesignerSpecies<?>>(identifier, result);
- }
-
- /**
- * Set structural state to species. StructuralState is a generic class with
- * some information about the species element.
- *
- * @param state
- * state to be set
- *
- * @param species
- * where the data should be saved
- */
- void processStateDataInSpecies(CellDesignerSpecies<?> species, SpeciesState state) {
- species.setHomodimer(state.getHomodimer());
-
- if (species instanceof CellDesignerComplexSpecies) {
- CellDesignerComplexSpecies complex = (CellDesignerComplexSpecies) species;
- complex.setStructuralState(state.getStructuralState());
- if (state.getModifications().size() != 0) {
- throw new NotImplementedException("Modification not supported in Complex");
- }
- } else if (species instanceof CellDesignerGene) {
- CellDesignerGene gene = (CellDesignerGene) species;
- if (state.getStructuralState() != null) {
- throw new NotImplementedException("StructuralState not supported in Gene");
- }
- for (CellDesignerModificationResidue mr : state.getModifications()) {
- gene.addModificationResidue(mr);
- }
- } else if (species instanceof CellDesignerProtein) {
- CellDesignerProtein<?> protein = (CellDesignerProtein<?>) species;
- protein.setStructuralState(state.getStructuralState());
- for (CellDesignerModificationResidue mr : state.getModifications()) {
- protein.addModificationResidue(mr);
- }
- } else if (species instanceof CellDesignerRna) {
- CellDesignerRna rna = (CellDesignerRna) species;
- if (state.getStructuralState() != null && !state.getStructuralState().isEmpty()) {
- throw new NotImplementedException("Structural state not supported in RNA");
- }
-
- for (CellDesignerModificationResidue mr : state.getModifications()) {
- rna.addRegion(createRnaRegion(mr));
- }
- } else if (species instanceof CellDesignerSimpleMolecule) {
- if (state.getStructuralState() != null && !state.getStructuralState().isEmpty()) {
- throw new NotImplementedException("Structural state not supported in SimpleMolecule");
- }
- if (state.getModifications().size() != 0) {
- throw new NotImplementedException("Modification not supported in SimpleMolecule");
- }
-
- } else if (species instanceof CellDesignerAntisenseRna) {
- CellDesignerAntisenseRna antisenseRna = (CellDesignerAntisenseRna) species;
- if (state.getStructuralState() != null && !state.getStructuralState().isEmpty()) {
- throw new NotImplementedException("Structural state not supported in AntisenseRna");
- }
-
- for (CellDesignerModificationResidue mr : state.getModifications()) {
- CellDesignerAntisenseRnaRegion region = createAntisenseRnaRegion(mr);
- antisenseRna.addRegion(region);
- }
- } else {
- if (state.getStructuralState() != null && !state.getStructuralState().isEmpty()) {
- throw new NotImplementedException("Structural state not supported in " + species.getClass().getSimpleName());
- }
- if (state.getModifications().size() != 0) {
- throw new NotImplementedException("Modification not supported in " + species.getClass().getSimpleName());
- }
- }
-
- }
-
- /**
- * Creates {@link SpeciesState} from xml node.
- *
- * @param stateNode
- * xml node
- * @return {@link SpeciesState} retrieved from xml node
- * @throws InvalidXmlSchemaException
- * thrown when xml node contains data that is not supported by xml
- * schema
- */
- private SpeciesState parseXmlSpeciesState(Node stateNode) throws InvalidXmlSchemaException {
- NodeList nodes = stateNode.getChildNodes();
- SpeciesState result = new SpeciesState();
- for (int x = 0; x < nodes.getLength(); x++) {
- Node node = nodes.item(x);
- if (node.getNodeType() == Node.ELEMENT_NODE) {
- if (node.getNodeName().equalsIgnoreCase("celldesigner:homodimer")) {
- result.setHomodimer(getNodeValue(node));
- } else if (node.getNodeName().equalsIgnoreCase("celldesigner:listOfStructuralStates")) {
- NodeList structureNodeList = node.getChildNodes();
- for (int y = 0; y < structureNodeList.getLength(); y++) {
- Node structureNode = structureNodeList.item(y);
- if (structureNode.getNodeType() == Node.ELEMENT_NODE) {
- if (structureNode.getNodeName().equalsIgnoreCase("celldesigner:structuralState")) {
- String state = getNodeAttr("structuralState", structureNode);
- result.setStructuralState(state);
- } else {
- throw new InvalidXmlSchemaException("Unknown element of celldesigner:listOfStructuralStates: " + node.getNodeName());
- }
-
- }
-
- }
-
- } else if (node.getNodeName().equalsIgnoreCase("celldesigner:listOfModifications")) {
- NodeList modificationNodeList = node.getChildNodes();
- for (int y = 0; y < modificationNodeList.getLength(); y++) {
- Node structureNode = modificationNodeList.item(y);
- if (structureNode.getNodeType() == Node.ELEMENT_NODE) {
- if (structureNode.getNodeName().equalsIgnoreCase("celldesigner:modification")) {
- CellDesignerModificationResidue modification = getSpeciesModification(structureNode);
-
- result.addModificationResidue(modification);
- } else {
- throw new InvalidXmlSchemaException("Unknown element of celldesigner:listOfModifications: " + node.getNodeName());
- }
- }
- }
- } else {
- throw new InvalidXmlSchemaException("Unknown element of celldesigner:state: " + node.getNodeName());
- }
- }
- }
- return result;
- }
-
- /**
- * Creates {@link CellDesignerModificationResidue} from the apropriate xml
- * node.
- *
- * @param rootNode
- * xml node
- * @return {@link CellDesignerModificationResidue} retrieved from the node
- * @throws InvalidXmlSchemaException
- * thrown when xml node contains data that is not supported by xml
- * schema
- */
- private CellDesignerModificationResidue getSpeciesModification(Node rootNode) throws InvalidXmlSchemaException {
- CellDesignerModificationResidue modification = new CellDesignerModificationResidue();
- modification.setIdModificationResidue(getNodeAttr("residue", rootNode));
- String state = getNodeAttr("state", rootNode);
- if (state != null) {
- ModificationState mState = ModificationState.getByName(state);
- if (mState == null) {
- throw new InvalidXmlSchemaException(
- "[" + modification.getClass().getSimpleName() + "\t" + modification.getIdModificationResidue() + "] Unknown modification state: " + state);
- }
- modification.setState(mState);
- }
- modification.setName(getNodeAttr("name", rootNode));
- modification.setSize(getNodeAttr("size", rootNode));
- modification.setAngle(getNodeAttr("pos", rootNode));
- NodeList list = rootNode.getChildNodes();
- for (int y = 0; y < list.getLength(); y++) {
- Node node = list.item(y);
- if (node.getNodeType() == Node.ELEMENT_NODE) {
- throw new InvalidXmlSchemaException(
- "[" + modification.getClass().getSimpleName() + "\t" + modification.getIdModificationResidue() + "] Unknown element of celldesigner:modification: "
- + node.getNodeName());
- }
- }
- return modification;
- }
-
- /**
- * Creates xml node representing {@link CellDesignerModificationResidue}.
- *
- * @param mr
- * object to be transformed into xml
- * @return xml node representing param object
- */
- private String modificationResidueToXml(CellDesignerModificationResidue mr) {
- String state = "";
- if (mr.getState() != null) {
- state = mr.getState().getFullName();
- }
- if (state == null || state.equals("")) {
- return "";
- }
- return "<celldesigner:modification residue=\"" + mr.getIdModificationResidue() + "\" state=\"" + state + "\"> </celldesigner:modification>\n";
- }
-
- /**
- * Creates {@link CellDesignerAntisenseRnaRegion} from
- * {@link CellDesignerModificationResidue} description.
- *
- * @param mr
- * object from which we create {@link CellDesignerAntisenseRnaRegion}
- * @return {@link CellDesignerAntisenseRnaRegion} object created from param
- */
- CellDesignerAntisenseRnaRegion createAntisenseRnaRegion(CellDesignerModificationResidue mr) {
- CellDesignerAntisenseRnaRegion region = new CellDesignerAntisenseRnaRegion();
- region.setIdAntisenseRnaRegion(mr.getIdModificationResidue());
- if (mr.getSize() != null) {
- region.setSize(mr.getSize());
- }
- region.setState(mr.getState());
- region.setName(mr.getName());
- if (mr.getAngle() != null) {
- region.setPos(mr.getAngle());
- }
- return region;
- }
-
- /**
- * Creates {@link CellDesignerRnaRegion} from
- * {@link CellDesignerModificationResidue} description.
- *
- * @param mr
- * object from which we create {@link CellDesignerRnaRegion}
- * @return {@link CellDesignerRnaRegion} object created from param
- */
- public CellDesignerRnaRegion createRnaRegion(CellDesignerModificationResidue mr) {
- CellDesignerRnaRegion result = new CellDesignerRnaRegion();
- result.setIdRnaRegion(mr.getIdModificationResidue());
- if (mr.getSize() != null) {
- result.setSize(mr.getSize());
- }
- result.setState(mr.getState());
- result.setName(mr.getName());
- if (mr.getAngle() != null) {
- result.setPos(mr.getAngle());
- }
- return result;
- }
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private Logger logger = Logger.getLogger(SpeciesSbmlParser.class.getName());
+
+ /**
+ * Collection of {@link CellDesignerElement cell designer elements} parsed from
+ * xml.
+ */
+ private CellDesignerElementCollection elements;
+
+ /**
+ * Default constructor. Model is required because some nodes require access to
+ * other parts of the model.
+ *
+ * @param elements
+ * collection of {@link CellDesignerElement cell designer elements}
+ * parsed from xml
+ */
+ public SpeciesSbmlParser(CellDesignerElementCollection elements) {
+ this.elements = elements;
+ }
+
+ @Override
+ public Pair<String, CellDesignerSpecies<?>> parseXmlElement(Node spieciesNode) throws InvalidXmlSchemaException {
+
+ NodeList list = spieciesNode.getChildNodes();
+
+ Node annotationNode = null;
+ Node notesNode = null;
+ for (int i = 0; i < list.getLength(); i++) {
+ Node node = list.item(i);
+ if (node.getNodeType() == Node.ELEMENT_NODE) {
+ if (node.getNodeName().equals("annotation")) {
+ annotationNode = node;
+ } else if (node.getNodeName().equals("notes")) {
+ notesNode = node;
+ } else {
+ throw new InvalidXmlSchemaException("Unknown element of annotation " + node.getNodeName());
+ }
+ }
+ }
+
+ if (annotationNode == null) {
+ throw new InvalidXmlSchemaException("No annotation node in SBML/model/listOfSpecies/species");
+ }
+
+ list = annotationNode.getChildNodes();
+ Node extensionNode = null;
+ Node rdfNode = null;
+
+ for (int i = 0; i < list.getLength(); i++) {
+ Node node = list.item(i);
+ if (node.getNodeType() == Node.ELEMENT_NODE) {
+ if (node.getNodeName().equals("celldesigner:extension")) {
+ extensionNode = node;
+ } else if (node.getNodeName().equals("rdf:RDF")) {
+ rdfNode = node;
+ } else {
+ throw new InvalidXmlSchemaException("Unknown element of annotation " + node.getNodeName());
+ }
+ }
+ }
+
+ if (extensionNode == null) {
+ throw new InvalidXmlSchemaException(
+ "No celldesigner:extension node in SBML/model/listOfSpecies/species/annotation");
+ }
+
+ list = extensionNode.getChildNodes();
+ Node speciesIdentity = null;
+ Node positionToCompartment = null;
+ for (int i = 0; i < list.getLength(); i++) {
+ Node node = list.item(i);
+ if (node.getNodeType() == Node.ELEMENT_NODE) {
+ if (node.getNodeName().equals("celldesigner:speciesIdentity")) {
+ speciesIdentity = node;
+ } else if (node.getNodeName().equals("celldesigner:positionToCompartment")) {
+ positionToCompartment = node;
+ } else if (node.getNodeName().equals("celldesigner:listOfCatalyzedReactions")) {
+ // we can ignore it - every node on the map contains information about
+ // itself
+ continue;
+ } else {
+ throw new InvalidXmlSchemaException("[" + getNodeAttr("id", spieciesNode)
+ + "]\tUnknown element of celldesigner:extension " + node.getNodeName());
+ }
+ }
+ }
+
+ if (speciesIdentity == null) {
+ throw new InvalidXmlSchemaException(
+ "No celldesigner:speciesIdentity node in SBML/model/listOfSpecies/species/annotation/extension");
+ }
+
+ Pair<String, CellDesignerSpecies<?>> result = parseSpeciesIdentity(speciesIdentity);
+
+ CellDesignerSpecies<?> species = result.getRight();
+ if (positionToCompartment != null) {
+ PositionToCompartment position = PositionToCompartment.getByString(getNodeValue(positionToCompartment));
+ if (position == null) {
+ throw new InvalidXmlSchemaException("Unknown position on compartment: " + getNodeValue(positionToCompartment));
+ }
+ species.setPositionToCompartment(position);
+ }
+
+ // we ignore metaid - it's useless and obstruct data model
+ // species.setMetaId(getNodeAttr("metaid", spieciesNode));
+ species.setElementId(getNodeAttr("id", spieciesNode));
+ species.setName(decodeName(getNodeAttr("name", spieciesNode)));
+ species.setInitialAmount(getNodeAttr("initialAmount", spieciesNode));
+ String substanceUnits = getNodeAttr("substanceUnits", spieciesNode);
+ if (substanceUnits != null && !substanceUnits.isEmpty()) {
+ species.setSubstanceUnits(SbmlUnitType.valueOf(substanceUnits.toUpperCase()));
+ }
+ species.setInitialAmount(getNodeAttr("initialAmount", spieciesNode));
+ species.setInitialConcentration(getNodeAttr("initialConcentration", spieciesNode));
+ species.setCharge(getNodeAttr("charge", spieciesNode));
+ species.setOnlySubstanceUnits(getNodeAttr("hasOnlySubstanceUnits", spieciesNode));
+ species.setBoundaryCondition(getNodeAttr("boundaryCondition", spieciesNode));
+ species.setConstant(getNodeAttr("constant", spieciesNode));
+
+ CellDesignerCompartment compartment = elements.getElementByElementId(getNodeAttr("compartment", spieciesNode));
+ if (compartment != null) {
+ species.setParent(compartment);
+ }
+
+ if (notesNode != null) {
+ species.setNotes(getRap().getNotes(notesNode));
+ }
+
+ if (rdfNode != null) {
+ XmlAnnotationParser xmlAnnotationParser = new XmlAnnotationParser();
+ species.addMiriamData(xmlAnnotationParser.parseRdfNode(annotationNode.getChildNodes()));
+ }
+
+ return result;
+ }
+
+ @Override
+ public String toXml(Species species) {
+ StringBuilder builder = new StringBuilder();
+ StringBuilder attributesBuilder = new StringBuilder();
+ attributesBuilder.append(" name=\"" + escapeXml(encodeName(species.getName())) + "\"");
+ attributesBuilder.append(" id=\"" + elements.getElementId(species) + "\"");
+ attributesBuilder.append(" metaid=\"" + elements.getElementId(species) + "\"");
+ if (species.getInitialAmount() != null) {
+ attributesBuilder.append(" initialAmount=\"" + species.getInitialAmount() + "\"");
+ }
+ if (species.getInitialConcentration() != null) {
+ attributesBuilder.append(" initialConcentration=\"" + species.getInitialConcentration() + "\"");
+ }
+ if (species.getCharge() != null) {
+ attributesBuilder.append(" charge=\"" + species.getCharge() + "\"");
+ }
+ if (species.hasOnlySubstanceUnits() != null) {
+ attributesBuilder.append(" hasOnlySubstanceUnits=\"" + species.hasOnlySubstanceUnits() + "\"");
+ }
+
+ Compartment comp = null;
+ // we have to exclude artifitial compartment aliases, becuase they aren't
+ // exported to CellDesigner file
+ if (species.getCompartment() != null && !(species.getCompartment() instanceof PathwayCompartment)) {
+ comp = species.getCompartment();
+ } else if (species.getComplex() == null) {
+ ModelData modelData = species.getModelData();
+ if (modelData != null) {
+ for (Compartment cAlias : modelData.getModel().getCompartments()) {
+ if (!(cAlias instanceof PathwayCompartment) && cAlias.cross(species)) {
+ if (comp == null) {
+ comp = cAlias;
+ } else if (comp.getSize() > cAlias.getSize()) {
+ comp = cAlias;
+ }
+ }
+ }
+ }
+ }
+
+ if (comp != null) {
+ attributesBuilder.append(" compartment=\"" + elements.getElementId(comp) + "\"");
+ } else {
+ attributesBuilder.append(" compartment=\"default\"");
+ }
+ builder.append("<species " + attributesBuilder.toString() + ">");
+
+ if ((species.getNotes() != null && !species.getNotes().equals("")) || species.getSymbol() != null
+ || species.getFullName() != null || species.getSynonyms().size() > 0) {
+ builder.append("<notes>");
+ builder.append("<html xmlns=\"http://www.w3.org/1999/xhtml\"><head><title/></head><body>");
+ RestAnnotationParser rap = new RestAnnotationParser();
+ builder.append(rap.createAnnotationString(species));
+ if (species.getNotes() != null) {
+ builder.append(species.getNotes());
+ }
+ builder.append("</body></html>");
+ builder.append("</notes>\n");
+ }
+ builder.append("<annotation>");
+ builder.append("<celldesigner:extension>");
+ if (species.getPositionToCompartment() != null) {
+ builder.append("<celldesigner:positionToCompartment>" + species.getPositionToCompartment().getStringName()
+ + "</celldesigner:positionToCompartment>");
+ }
+ builder.append(speciesIdentityToXml(species));
+
+ builder.append("</celldesigner:extension>\n");
+
+ XmlAnnotationParser xmlAnnotationParser = new XmlAnnotationParser();
+ builder.append(xmlAnnotationParser.dataSetToXmlString(species.getMiriamData()));
+
+ builder.append("</annotation>\n");
+
+ builder.append("</species>\n");
+ return builder.toString();
+ }
+
+ /**
+ * Creates speciesIdentity xml node for the {@link CellDesignerSpecies}.
+ *
+ * @param species
+ * species to be transformed into xml
+ * @return speciesIdentity xml node
+ */
+ String speciesIdentityToXml(Species species) {
+ StringBuilder sb = new StringBuilder();
+ String classType = "";
+ SpeciesMapping mapping = SpeciesMapping.getMappingByModelClass(species.getClass());
+ if (mapping != null) {
+ classType = mapping.getCellDesignerString();
+ } else {
+ throw new InvalidArgumentException("Invalid species class type: " + species.getClass().getName());
+ }
+ sb.append("<celldesigner:speciesIdentity>");
+ sb.append("<celldesigner:class>" + classType + "</celldesigner:class>\n");
+ if (species instanceof Rna) {
+ sb.append("<celldesigner:rnaReference>r_" + elements.getElementId(species) + "</celldesigner:rnaReference>\n");
+ } else if (species instanceof Protein) {
+ sb.append(
+ "<celldesigner:proteinReference>p_" + elements.getElementId(species) + "</celldesigner:proteinReference>\n");
+ } else if (species instanceof Gene) {
+ sb.append("<celldesigner:geneReference>g_" + elements.getElementId(species) + "</celldesigner:geneReference>\n");
+ } else if (species instanceof AntisenseRna) {
+ sb.append("<celldesigner:antisensernaReference>ar_" + elements.getElementId(species)
+ + "</celldesigner:antisensernaReference>\n");
+ }
+ SpeciesState state = new SpeciesState(species);
+ sb.append(speciesStateToXml(state));
+ sb.append("<celldesigner:name>" + escapeXml(encodeName(species.getName())) + "</celldesigner:name>\n");
+
+ Boolean hypothetical = species.getHypothetical();
+ if (hypothetical != null) {
+ sb.append("<celldesigner:hypothetical>" + hypothetical + "</celldesigner:hypothetical>\n");
+ }
+
+ sb.append("</celldesigner:speciesIdentity>\n");
+ return sb.toString();
+ }
+
+ /**
+ * Creates CellDesigner species state into xml node.
+ *
+ * @param state
+ * state of the species.
+ * @return CellDesigner xml node used for description of the state
+ */
+ String speciesStateToXml(SpeciesState state) {
+ StringBuilder sb = new StringBuilder();
+ if (state.getHomodimer() != 1) {
+ sb.append("<celldesigner:homodimer>" + state.getHomodimer() + "</celldesigner:homodimer>\n");
+ }
+ if (state.getStructuralState() != null && !state.getStructuralState().equals("")) {
+ sb.append("<celldesigner:listOfStructuralStates>\n");
+ sb.append("<celldesigner:structuralState structuralState=\"" + state.getStructuralState() + "\">"
+ + state.getStructuralState() + "</celldesigner:structuralState>");
+ sb.append("</celldesigner:listOfStructuralStates>\n");
+ }
+ if (state.getModifications().size() > 0) {
+ sb.append("<celldesigner:listOfModifications>\n");
+ for (CellDesignerModificationResidue mr : state.getModifications()) {
+ sb.append(modificationResidueToXml(mr));
+ }
+ sb.append("</celldesigner:listOfModifications>\n");
+ }
+ if (sb.length() > 0) {
+ sb.insert(0, "<celldesigner:state>\n");
+ sb.append("</celldesigner:state>\n");
+ }
+ return sb.toString();
+ }
+
+ /**
+ * Parses CellDesigner SpeciesIdentity node into {@link CellDesignerSpecies}.
+ *
+ * @param rootNode
+ * xml node to parse
+ * @return {@link Pair} of Species retrieved from SpeciesIdentity node and
+ * CellDesigner identifier
+ * @throws InvalidXmlSchemaException
+ * thrown when there is a problem with xml
+ */
+ public Pair<String, CellDesignerSpecies<?>> parseSpeciesIdentity(Node rootNode) throws InvalidXmlSchemaException {
+ NodeList nodes = rootNode.getChildNodes();
+ CellDesignerSpecies<?> result = new CellDesignerSpecies<Species>();
+ Node classNode = getNode("celldesigner:class", nodes);
+ if (classNode == null) {
+ throw new InvalidXmlSchemaException("Species node in Sbml model doesn't contain node \"celldesigner:class\".");
+ } else {
+ String value = getNodeValue(classNode);
+ SpeciesMapping mapping = SpeciesMapping.getMappingByString(value);
+ if (mapping != null) {
+ result = mapping.createSpecies(result);
+ } else {
+ throw new InvalidXmlSchemaException("Species node in Sbml model is of unknown type: " + value);
+ }
+ }
+ String identifier = "";
+ for (int x = 0; x < nodes.getLength(); x++) {
+ Node node = nodes.item(x);
+ if (node.getNodeType() == Node.ELEMENT_NODE) {
+ if (node.getNodeName().equalsIgnoreCase("celldesigner:class")) {
+ continue;
+ } else if (node.getNodeName().equalsIgnoreCase("celldesigner:proteinReference")) {
+ if (result instanceof CellDesignerProtein) {
+ identifier = getNodeValue(node);
+ } else {
+ throw new InvalidXmlSchemaException(
+ "Wrong class type for protein reference: " + result.getClass().getName());
+ }
+ } else if (node.getNodeName().equalsIgnoreCase("celldesigner:geneReference")) {
+ if (result instanceof CellDesignerGene) {
+ identifier = getNodeValue(node);
+ } else {
+ throw new InvalidXmlSchemaException("Wrong class type for gene reference: " + result.getClass().getName());
+ }
+ } else if (node.getNodeName().equalsIgnoreCase("celldesigner:rnaReference")) {
+ if (result instanceof CellDesignerRna) {
+ identifier = getNodeValue(node);
+ } else {
+ throw new InvalidXmlSchemaException("Wrong class type for rna reference: " + result.getClass().getName());
+ }
+ } else if (node.getNodeName().equalsIgnoreCase("celldesigner:antisensernaReference")) {
+ if (result instanceof CellDesignerAntisenseRna) {
+ identifier = getNodeValue(node);
+ } else {
+ throw new InvalidXmlSchemaException(
+ "Wrong class type for antisense rna reference: " + result.getClass().getName());
+ }
+ } else if (node.getNodeName().equalsIgnoreCase("celldesigner:hypothetical")) {
+ result.setHypothetical(getNodeValue(node));
+ } else if (node.getNodeName().equalsIgnoreCase("celldesigner:name")) {
+ result.setName(decodeName(getNodeValue(node)));
+ } else if (node.getNodeName().equalsIgnoreCase("celldesigner:state")) {
+ SpeciesState state = parseXmlSpeciesState(node);
+ processStateDataInSpecies(result, state);
+ } else {
+ throw new InvalidXmlSchemaException("Unknown element of celldesigner:speciesIdentity: " + node.getNodeName());
+ }
+ }
+
+ }
+ return new Pair<String, CellDesignerSpecies<?>>(identifier, result);
+ }
+
+ /**
+ * Set structural state to species. StructuralState is a generic class with some
+ * information about the species element.
+ *
+ * @param state
+ * state to be set
+ *
+ * @param species
+ * where the data should be saved
+ */
+ void processStateDataInSpecies(CellDesignerSpecies<?> species, SpeciesState state) {
+ species.setHomodimer(state.getHomodimer());
+
+ if (species instanceof CellDesignerComplexSpecies) {
+ CellDesignerComplexSpecies complex = (CellDesignerComplexSpecies) species;
+ complex.setStructuralState(state.getStructuralState());
+ if (state.getModifications().size() != 0) {
+ throw new NotImplementedException("Modification not supported in Complex");
+ }
+ } else if (species instanceof CellDesignerGene) {
+ CellDesignerGene gene = (CellDesignerGene) species;
+ if (state.getStructuralState() != null) {
+ throw new NotImplementedException("StructuralState not supported in Gene");
+ }
+ for (CellDesignerModificationResidue mr : state.getModifications()) {
+ gene.addModificationResidue(mr);
+ }
+ } else if (species instanceof CellDesignerProtein) {
+ CellDesignerProtein<?> protein = (CellDesignerProtein<?>) species;
+ protein.setStructuralState(state.getStructuralState());
+ for (CellDesignerModificationResidue mr : state.getModifications()) {
+ protein.addModificationResidue(mr);
+ }
+ } else if (species instanceof CellDesignerRna) {
+ CellDesignerRna rna = (CellDesignerRna) species;
+ if (state.getStructuralState() != null && !state.getStructuralState().isEmpty()) {
+ throw new NotImplementedException("Structural state not supported in RNA");
+ }
+
+ for (CellDesignerModificationResidue mr : state.getModifications()) {
+ rna.addRegion(createRnaRegion(mr));
+ }
+ } else if (species instanceof CellDesignerSimpleMolecule) {
+ if (state.getStructuralState() != null && !state.getStructuralState().isEmpty()) {
+ throw new NotImplementedException("Structural state not supported in SimpleMolecule");
+ }
+ if (state.getModifications().size() != 0) {
+ throw new NotImplementedException("Modification not supported in SimpleMolecule");
+ }
+
+ } else if (species instanceof CellDesignerAntisenseRna) {
+ CellDesignerAntisenseRna antisenseRna = (CellDesignerAntisenseRna) species;
+ if (state.getStructuralState() != null && !state.getStructuralState().isEmpty()) {
+ throw new NotImplementedException("Structural state not supported in AntisenseRna");
+ }
+
+ for (CellDesignerModificationResidue mr : state.getModifications()) {
+ CellDesignerAntisenseRnaRegion region = createAntisenseRnaRegion(mr);
+ antisenseRna.addRegion(region);
+ }
+ } else {
+ if (state.getStructuralState() != null && !state.getStructuralState().isEmpty()) {
+ throw new NotImplementedException("Structural state not supported in " + species.getClass().getSimpleName());
+ }
+ if (state.getModifications().size() != 0) {
+ throw new NotImplementedException("Modification not supported in " + species.getClass().getSimpleName());
+ }
+ }
+
+ }
+
+ /**
+ * Creates {@link SpeciesState} from xml node.
+ *
+ * @param stateNode
+ * xml node
+ * @return {@link SpeciesState} retrieved from xml node
+ * @throws InvalidXmlSchemaException
+ * thrown when xml node contains data that is not supported by xml
+ * schema
+ */
+ private SpeciesState parseXmlSpeciesState(Node stateNode) throws InvalidXmlSchemaException {
+ NodeList nodes = stateNode.getChildNodes();
+ SpeciesState result = new SpeciesState();
+ for (int x = 0; x < nodes.getLength(); x++) {
+ Node node = nodes.item(x);
+ if (node.getNodeType() == Node.ELEMENT_NODE) {
+ if (node.getNodeName().equalsIgnoreCase("celldesigner:homodimer")) {
+ result.setHomodimer(getNodeValue(node));
+ } else if (node.getNodeName().equalsIgnoreCase("celldesigner:listOfStructuralStates")) {
+ NodeList structureNodeList = node.getChildNodes();
+ for (int y = 0; y < structureNodeList.getLength(); y++) {
+ Node structureNode = structureNodeList.item(y);
+ if (structureNode.getNodeType() == Node.ELEMENT_NODE) {
+ if (structureNode.getNodeName().equalsIgnoreCase("celldesigner:structuralState")) {
+ String state = getNodeAttr("structuralState", structureNode);
+ result.setStructuralState(state);
+ } else {
+ throw new InvalidXmlSchemaException(
+ "Unknown element of celldesigner:listOfStructuralStates: " + node.getNodeName());
+ }
+
+ }
+
+ }
+
+ } else if (node.getNodeName().equalsIgnoreCase("celldesigner:listOfModifications")) {
+ NodeList modificationNodeList = node.getChildNodes();
+ for (int y = 0; y < modificationNodeList.getLength(); y++) {
+ Node structureNode = modificationNodeList.item(y);
+ if (structureNode.getNodeType() == Node.ELEMENT_NODE) {
+ if (structureNode.getNodeName().equalsIgnoreCase("celldesigner:modification")) {
+ CellDesignerModificationResidue modification = getSpeciesModification(structureNode);
+
+ result.addModificationResidue(modification);
+ } else {
+ throw new InvalidXmlSchemaException(
+ "Unknown element of celldesigner:listOfModifications: " + node.getNodeName());
+ }
+ }
+ }
+ } else {
+ throw new InvalidXmlSchemaException("Unknown element of celldesigner:state: " + node.getNodeName());
+ }
+ }
+ }
+ return result;
+ }
+
+ /**
+ * Creates {@link CellDesignerModificationResidue} from the apropriate xml node.
+ *
+ * @param rootNode
+ * xml node
+ * @return {@link CellDesignerModificationResidue} retrieved from the node
+ * @throws InvalidXmlSchemaException
+ * thrown when xml node contains data that is not supported by xml
+ * schema
+ */
+ private CellDesignerModificationResidue getSpeciesModification(Node rootNode) throws InvalidXmlSchemaException {
+ CellDesignerModificationResidue modification = new CellDesignerModificationResidue();
+ modification.setIdModificationResidue(getNodeAttr("residue", rootNode));
+ String state = getNodeAttr("state", rootNode);
+ if (state != null) {
+ ModificationState mState = ModificationState.getByName(state);
+ if (mState == null) {
+ throw new InvalidXmlSchemaException("[" + modification.getClass().getSimpleName() + "\t"
+ + modification.getIdModificationResidue() + "] Unknown modification state: " + state);
+ }
+ modification.setState(mState);
+ }
+ modification.setName(getNodeAttr("name", rootNode));
+ modification.setSize(getNodeAttr("size", rootNode));
+ modification.setAngle(getNodeAttr("pos", rootNode));
+ NodeList list = rootNode.getChildNodes();
+ for (int y = 0; y < list.getLength(); y++) {
+ Node node = list.item(y);
+ if (node.getNodeType() == Node.ELEMENT_NODE) {
+ throw new InvalidXmlSchemaException(
+ "[" + modification.getClass().getSimpleName() + "\t" + modification.getIdModificationResidue()
+ + "] Unknown element of celldesigner:modification: " + node.getNodeName());
+ }
+ }
+ return modification;
+ }
+
+ /**
+ * Creates xml node representing {@link CellDesignerModificationResidue}.
+ *
+ * @param mr
+ * object to be transformed into xml
+ * @return xml node representing param object
+ */
+ private String modificationResidueToXml(CellDesignerModificationResidue mr) {
+ String state = "";
+ if (mr.getState() != null) {
+ state = mr.getState().getFullName();
+ }
+ if (state == null || state.equals("")) {
+ return "";
+ }
+ return "<celldesigner:modification residue=\"" + mr.getIdModificationResidue() + "\" state=\"" + state
+ + "\"> </celldesigner:modification>\n";
+ }
+
+ /**
+ * Creates {@link CellDesignerAntisenseRnaRegion} from
+ * {@link CellDesignerModificationResidue} description.
+ *
+ * @param mr
+ * object from which we create {@link CellDesignerAntisenseRnaRegion}
+ * @return {@link CellDesignerAntisenseRnaRegion} object created from param
+ */
+ CellDesignerAntisenseRnaRegion createAntisenseRnaRegion(CellDesignerModificationResidue mr) {
+ CellDesignerAntisenseRnaRegion region = new CellDesignerAntisenseRnaRegion();
+ region.setIdAntisenseRnaRegion(mr.getIdModificationResidue());
+ if (mr.getSize() != null) {
+ region.setSize(mr.getSize());
+ }
+ region.setState(mr.getState());
+ region.setName(mr.getName());
+ if (mr.getAngle() != null) {
+ region.setPos(mr.getAngle());
+ }
+ return region;
+ }
+
+ /**
+ * Creates {@link CellDesignerRnaRegion} from
+ * {@link CellDesignerModificationResidue} description.
+ *
+ * @param mr
+ * object from which we create {@link CellDesignerRnaRegion}
+ * @return {@link CellDesignerRnaRegion} object created from param
+ */
+ public CellDesignerRnaRegion createRnaRegion(CellDesignerModificationResidue mr) {
+ CellDesignerRnaRegion result = new CellDesignerRnaRegion();
+ result.setIdRnaRegion(mr.getIdModificationResidue());
+ if (mr.getSize() != null) {
+ result.setSize(mr.getSize());
+ }
+ result.setState(mr.getState());
+ result.setName(mr.getName());
+ if (mr.getAngle() != null) {
+ result.setPos(mr.getAngle());
+ }
+ return result;
+ }
}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerGenericProtein.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerGenericProtein.java
index 84bca8ce5c144fab25ec3f04e390c4ad3f494166..a7625eefba91483854df0fb927b5eb844ab9cb49 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerGenericProtein.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerGenericProtein.java
@@ -13,60 +13,59 @@ import lcsb.mapviewer.model.map.species.GenericProtein;
*/
public class CellDesignerGenericProtein extends CellDesignerProtein<GenericProtein> {
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private transient Logger logger = Logger.getLogger(CellDesignerGenericProtein.class);
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private transient Logger logger = Logger.getLogger(CellDesignerGenericProtein.class);
- /**
- *
- */
- private static final long serialVersionUID = 1L;
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
- /**
- * Default constructor.
- */
- public CellDesignerGenericProtein() {
- super();
- }
+ /**
+ * Default constructor.
+ */
+ public CellDesignerGenericProtein() {
+ super();
+ }
- /**
- * Constructor that creates a copy of species.
- *
- * @param species
- * original species
- */
- public CellDesignerGenericProtein(CellDesignerSpecies<?> species) {
- super(species);
- }
+ /**
+ * Constructor that creates a copy of species.
+ *
+ * @param species
+ * original species
+ */
+ public CellDesignerGenericProtein(CellDesignerSpecies<?> species) {
+ super(species);
+ }
- /**
- * Deafult constructor.
- *
- * @param id
- * identifier of the protein
- */
- public CellDesignerGenericProtein(String id) {
- setElementId(id);
- setName(id);
- }
+ /**
+ * Default constructor.
+ *
+ * @param id
+ * identifier of the protein
+ */
+ public CellDesignerGenericProtein(String id) {
+ setElementId(id);
+ setName(id);
+ }
- @Override
- public CellDesignerGenericProtein copy() {
- if (this.getClass().equals(CellDesignerGenericProtein.class)) {
- return new CellDesignerGenericProtein(this);
- } else {
- throw new NotImplementedException("Copy method for " + this.getClass() + " class not implemented");
- }
- }
+ @Override
+ public CellDesignerGenericProtein copy() {
+ if (this.getClass().equals(CellDesignerGenericProtein.class)) {
+ return new CellDesignerGenericProtein(this);
+ } else {
+ throw new NotImplementedException("Copy method for " + this.getClass() + " class not implemented");
+ }
+ }
- @Override
- public GenericProtein createModelElement(String aliasId) {
- GenericProtein result = new GenericProtein(aliasId);
- super.setModelObjectFields(result);
-
- return result;
- }
+ @Override
+ public GenericProtein createModelElement(String aliasId) {
+ GenericProtein result = new GenericProtein(aliasId);
+ super.setModelObjectFields(result);
+ return result;
+ }
}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerProtein.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerProtein.java
index d94a1dc5381972c8515bccb8a85325e9e152da04..ae3677e954e3caf411d5af7276fedbabf42cfaf8 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerProtein.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerProtein.java
@@ -18,136 +18,136 @@ import lcsb.mapviewer.model.map.species.Protein;
*
*/
public class CellDesignerProtein<T extends Protein> extends CellDesignerSpecies<T> {
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Default class logger.
- */
- private static Logger logger = Logger.getLogger(CellDesignerProtein.class.getName());
-
- /**
- * State of the protein.
- */
- private String structuralState = null;
-
- /**
- * List of modifications for the Protein.
- */
- private List<CellDesignerModificationResidue> modificationResidues = new ArrayList<CellDesignerModificationResidue>();
-
- /**
- * Constructor that initializes protein with the data passed in the argument.
- *
- * @param species
- * original species used for data initialization
- */
- public CellDesignerProtein(CellDesignerSpecies<?> species) {
- super(species);
- if (species instanceof CellDesignerProtein) {
- CellDesignerProtein<?> protein = (CellDesignerProtein<?>) species;
- if (protein.getStructuralState() != null) {
- setStructuralState(new String(protein.getStructuralState()));
- }
- for (CellDesignerModificationResidue mr : protein.getModificationResidues()) {
- addModificationResidue(new CellDesignerModificationResidue(mr));
- }
- }
- }
-
- @Override
- public void update(CellDesignerSpecies<?> species) {
- super.update(species);
- if (species instanceof CellDesignerProtein) {
- CellDesignerProtein<?> protein = (CellDesignerProtein<?>) species;
- if (getStructuralState() == null || getStructuralState().equals("")) {
- setStructuralState(protein.getStructuralState());
- }
- for (CellDesignerModificationResidue mr : protein.getModificationResidues()) {
- addModificationResidue(mr);
- }
- }
- }
-
- /**
- * Default constructor.
- */
- public CellDesignerProtein() {
- super();
- }
-
- @Override
- public CellDesignerProtein<T> copy() {
- if (this.getClass().equals(CellDesignerProtein.class)) {
- return new CellDesignerProtein<T>(this);
- } else {
- throw new NotImplementedException("Copy method for " + this.getClass() + " class not implemented");
- }
- }
-
- /**
- * Adds modification to the protein.
- *
- * @param modificationResidue
- * modification to add
- */
- public void addModificationResidue(CellDesignerModificationResidue modificationResidue) {
- for (CellDesignerModificationResidue mr : modificationResidues) {
- if (mr.getIdModificationResidue().equals(modificationResidue.getIdModificationResidue())) {
- mr.update(modificationResidue);
- return;
- }
- }
- modificationResidues.add(modificationResidue);
- modificationResidue.setSpecies(this);
- }
-
- /**
- * @return the structuralState
- * @see #structuralState
- */
- public String getStructuralState() {
- return structuralState;
- }
-
- /**
- * @param structuralState
- * the structuralState to set
- * @see #structuralState
- */
- public void setStructuralState(String structuralState) {
- if (this.structuralState != null && !this.structuralState.equals("") && !this.structuralState.equals(structuralState)) {
- logger.warn("replacing structural state, Old: " + this.structuralState + " into new: " + structuralState);
- }
- this.structuralState = structuralState;
- }
-
- /**
- * @return the modificationResidues
- * @see #modificationResidues
- */
- public List<CellDesignerModificationResidue> getModificationResidues() {
- return modificationResidues;
- }
-
- /**
- * @param modificationResidues
- * the modificationResidues to set
- * @see #modificationResidues
- */
- public void setModificationResidues(List<CellDesignerModificationResidue> modificationResidues) {
- this.modificationResidues = modificationResidues;
- }
-
- @Override
- protected void setModelObjectFields(T result) {
- super.setModelObjectFields(result);
- result.setStructuralState(structuralState);
- for (CellDesignerModificationResidue mr : modificationResidues) {
- result.addModificationResidue(mr.createModificationResidueAlias());
- }
- }
-
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Default class logger.
+ */
+ private static Logger logger = Logger.getLogger(CellDesignerProtein.class.getName());
+
+ /**
+ * State of the protein.
+ */
+ private String structuralState = null;
+
+ /**
+ * List of modifications for the Protein.
+ */
+ private List<CellDesignerModificationResidue> modificationResidues = new ArrayList<CellDesignerModificationResidue>();
+
+ /**
+ * Constructor that initializes protein with the data passed in the argument.
+ *
+ * @param species
+ * original species used for data initialization
+ */
+ public CellDesignerProtein(CellDesignerSpecies<?> species) {
+ super(species);
+ if (species instanceof CellDesignerProtein) {
+ CellDesignerProtein<?> protein = (CellDesignerProtein<?>) species;
+ if (protein.getStructuralState() != null) {
+ setStructuralState(new String(protein.getStructuralState()));
+ }
+ for (CellDesignerModificationResidue mr : protein.getModificationResidues()) {
+ addModificationResidue(new CellDesignerModificationResidue(mr));
+ }
+ }
+ }
+
+ @Override
+ public void update(CellDesignerSpecies<?> species) {
+ super.update(species);
+ if (species instanceof CellDesignerProtein) {
+ CellDesignerProtein<?> protein = (CellDesignerProtein<?>) species;
+ if (getStructuralState() == null || getStructuralState().equals("")) {
+ setStructuralState(protein.getStructuralState());
+ }
+ for (CellDesignerModificationResidue mr : protein.getModificationResidues()) {
+ addModificationResidue(mr);
+ }
+ }
+ }
+
+ /**
+ * Default constructor.
+ */
+ public CellDesignerProtein() {
+ super();
+ }
+
+ @Override
+ public CellDesignerProtein<T> copy() {
+ if (this.getClass().equals(CellDesignerProtein.class)) {
+ return new CellDesignerProtein<T>(this);
+ } else {
+ throw new NotImplementedException("Copy method for " + this.getClass() + " class not implemented");
+ }
+ }
+
+ /**
+ * Adds modification to the protein.
+ *
+ * @param modificationResidue
+ * modification to add
+ */
+ public void addModificationResidue(CellDesignerModificationResidue modificationResidue) {
+ for (CellDesignerModificationResidue mr : modificationResidues) {
+ if (mr.getIdModificationResidue().equals(modificationResidue.getIdModificationResidue())) {
+ mr.update(modificationResidue);
+ return;
+ }
+ }
+ modificationResidues.add(modificationResidue);
+ modificationResidue.setSpecies(this);
+ }
+
+ /**
+ * @return the structuralState
+ * @see #structuralState
+ */
+ public String getStructuralState() {
+ return structuralState;
+ }
+
+ /**
+ * @param structuralState
+ * the structuralState to set
+ * @see #structuralState
+ */
+ public void setStructuralState(String structuralState) {
+ if (this.structuralState != null && !this.structuralState.equals("")
+ && !this.structuralState.equals(structuralState)) {
+ logger.warn("replacing structural state, Old: " + this.structuralState + " into new: " + structuralState);
+ }
+ this.structuralState = structuralState;
+ }
+
+ /**
+ * @return the modificationResidues
+ * @see #modificationResidues
+ */
+ public List<CellDesignerModificationResidue> getModificationResidues() {
+ return modificationResidues;
+ }
+
+ /**
+ * @param modificationResidues
+ * the modificationResidues to set
+ * @see #modificationResidues
+ */
+ public void setModificationResidues(List<CellDesignerModificationResidue> modificationResidues) {
+ this.modificationResidues = modificationResidues;
+ }
+
+ @Override
+ protected void setModelObjectFields(T result) {
+ super.setModelObjectFields(result);
+ result.setStructuralState(structuralState);
+ for (CellDesignerModificationResidue mr : modificationResidues) {
+ result.addModificationResidue(mr.createModificationResidueAlias());
+ }
+ }
}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerSpecies.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerSpecies.java
index a9b87f73c5f5531f5742b9b572f4a03b97686bd0..c28f67f2e13fef25719339fa268d4b0efd1ffe1e 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerSpecies.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerSpecies.java
@@ -5,6 +5,7 @@ import org.apache.log4j.Logger;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.common.exception.NotImplementedException;
import lcsb.mapviewer.model.map.MiriamData;
+import lcsb.mapviewer.model.map.kinetics.SbmlUnitType;
import lcsb.mapviewer.model.map.species.Species;
import lcsb.mapviewer.model.map.species.field.PositionToCompartment;
@@ -17,464 +18,511 @@ import lcsb.mapviewer.model.map.species.field.PositionToCompartment;
*
*/
public class CellDesignerSpecies<T extends Species> extends CellDesignerElement<T> {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Default class logger.
- */
- private static Logger logger = Logger.getLogger(CellDesignerSpecies.class.getName());
-
- /**
- * Identifier of the species. It must be unique within the model.
- */
- private String idSpecies;
-
- /**
- * Initial amount of species.
- */
- private Integer initialAmount = null;
-
- /**
- * Charge of the species.
- */
- private Integer charge = null;
-
- /**
- * Initial concentration of species.
- */
- private Integer initialConcentration = null;
-
- /**
- * Is only substance units allowed.
- */
- private Boolean onlySubstanceUnits = null;
-
- /**
- * How many dimers are in this species.
- */
- private int homodimer = 1;
-
- /**
- * Position on the compartment.
- */
- private PositionToCompartment positionToCompartment = null;
-
- /**
- * Is species hypothetical.
- */
- private Boolean hypothetical = null;
-
- /**
- * Set hypothetical flag from text input.
- *
- * @param text
- * string with true/false value that determines hypothetical state.
- * @see #hypothetical
- */
- public void setHypothetical(String text) {
- hypothetical = text.equals("true");
- }
-
- /**
- * Constructor that copies the data from species given in the argument.
- *
- * @param species
- * parent species from which we want to copy data
- */
- public CellDesignerSpecies(CellDesignerSpecies<?> species) {
- super(species);
- this.hypothetical = species.hypothetical;
- this.idSpecies = species.idSpecies;
- this.positionToCompartment = species.positionToCompartment;
- this.initialAmount = species.initialAmount;
- this.charge = species.charge;
- this.initialConcentration = species.initialConcentration;
- this.onlySubstanceUnits = species.onlySubstanceUnits;
- this.homodimer = species.homodimer;
- }
-
- /**
- * Default constructor.
- */
- public CellDesignerSpecies() {
- super();
- idSpecies = "";
- }
-
- /**
- * Default constructor with species identifier as a parameter.
- *
- * @param id
- * species identifier
- */
- public CellDesignerSpecies(String id) {
- this();
- this.idSpecies = id;
- this.setName(id);
- }
-
- @Override
- public CellDesignerSpecies<T> copy() {
- CellDesignerSpecies<T> result = new CellDesignerSpecies<T>(this);
-
- result.idSpecies = idSpecies;
- result.setNotes(getNotes());
- result.setHypothetical(hypothetical);
- // correct this
-
- result.setParent(getParent());
-
- result.charge = charge;
- result.initialAmount = initialAmount;
- result.initialConcentration = initialConcentration;
- result.onlySubstanceUnits = onlySubstanceUnits;
- result.positionToCompartment = positionToCompartment;
- result.homodimer = homodimer;
- return result;
- }
-
- /**
- * Updates species with the value from the species given in the parameter.
- *
- * @param species
- * object from which we are updating information
- */
- public void update(CellDesignerSpecies<?> species) {
- if (getName() == null || getName().equals("")) {
- setName(species.getName());
- } else if (!getName().trim().equals(species.getName().trim())) {
- String id = species.getElementId();
- if (id == null || id.equals("")) {
- id = getElementId();
- }
- logger.warn("Two different names in species with id =" + id + ": \"" + species.getName() + "\", \"" + getName() + "\"");
- setName(species.getName());
- }
- if (idSpecies == null || idSpecies.equals("")) {
- setElementId(species.getElementId());
- }
- for (MiriamData md : species.getMiriamData()) {
- if (!getMiriamData().contains(md)) {
- addMiriamData(new MiriamData(md));
- }
- }
- if (this.getNotes() == null || this.getNotes().trim().equals("")) {
- setNotes(species.getNotes());
- } else if (species.getNotes() != null && !species.getNotes().trim().equals("") && !this.getNotes().equals(species.getNotes())) {
- String string1 = this.getNotes();
-
- String string2 = species.getNotes();
-
- string1 = string1.trim();
- string2 = string2.trim();
- if (string2.toLowerCase().contains(string1.toLowerCase())) {
- setNotes(species.getNotes());
- } else if (!string1.toLowerCase().contains(string2.toLowerCase())) {
- // insert new information
- setNotes(string2 + getNotes());
- }
- }
-
- if (getParent() == null) {
- setParent(species.getParent());
- }
-
- if (species.getHypothetical() != null) {
- setHypothetical(species.getHypothetical());
- }
-
- if (getSymbol() != null && !getSymbol().equals("")) {
- if (species.getSymbol() != null && !species.getSymbol().equals("")) {
- if (!species.getSymbol().equals(getSymbol())) {
- logger.warn("Different symbol names: " + species.getSymbol() + ", " + getSymbol() + ". Ignoring...");
- }
- }
- } else {
- setSymbol(species.getSymbol());
- }
-
- if (getFullName() != null && !getFullName().equals("")) {
- if (species.getFullName() != null && !species.getFullName().equals("")) {
- if (!species.getFullName().equals(getFullName())) {
- logger.warn("Different symbol names: " + species.getFullName() + ", " + getFullName() + ". Ignoring...");
- }
- }
- } else {
- setFullName(species.getFullName());
- }
-
- for (String string : species.getSynonyms()) {
- if (!getSynonyms().contains(string)) {
- getSynonyms().add(string);
- }
- }
-
- for (String string : species.getFormerSymbols()) {
- if (!getFormerSymbols().contains(string)) {
- getFormerSymbols().add(string);
- }
- }
- if (species.getHomodimer() != 1) {
- setHomodimer(species.getHomodimer());
- }
- }
-
- /**
- * Sets initial amount from text.
- *
- * @param text
- * initial amount in string format
- * @see #initialAmount
- */
-
- public void setInitialAmount(String text) {
- if (text != null && !text.trim().equals("")) {
- try {
- initialAmount = Integer.parseInt(text);
- } catch (NumberFormatException e) {
- throw new InvalidArgumentException("Invalid species amount: " + text, e);
- }
- } else {
- initialAmount = null;
- }
-
- }
-
- /**
- * Sets charge from text.
- *
- * @param text
- * charge in string format
- * @see #charge
- */
- public void setCharge(String text) {
- if (text != null && !text.trim().equals("")) {
- try {
- charge = Integer.parseInt(text);
- } catch (NumberFormatException e) {
- throw new InvalidArgumentException("Invalid species charge: " + text, e);
- }
- } else {
- charge = null;
- }
-
- }
-
- /**
- * Sets OnlySubstanceUnits amount from text.
- *
- * @param text
- * OnlySubstanceUnits in string format
- * @see #onlySubstanceUnits
- */
- public void setOnlySubstanceUnits(String text) {
- if (text != null && !text.trim().equals("")) {
- if (text.equalsIgnoreCase("TRUE")) {
- onlySubstanceUnits = true;
- } else if (text.equalsIgnoreCase("FALSE")) {
- onlySubstanceUnits = false;
- } else {
- throw new InvalidArgumentException("Invalid species value for only substance unit boolean: " + text);
- }
- } else {
- onlySubstanceUnits = null;
- }
- }
-
- /**
- * Sets initial concentration amount from text.
- *
- * @param text
- * initial concentration in string format
- * @see #initialConcentration
- */
- public void setInitialConcentration(String text) {
- if (text != null && !text.trim().equals("")) {
- try {
- initialConcentration = Integer.parseInt(text);
- } catch (NumberFormatException e) {
- throw new InvalidArgumentException("Invalid species initial concentration: " + text, e);
- }
- } else {
- initialConcentration = null;
- }
- }
-
- /**
- * Is species hypothetical or not.
- *
- * @return <code>true</code> if species is hypothetical, <code>false</code>
- * otherwise
- */
- public boolean isHypothetical() {
- if (hypothetical == null) {
- return false;
- }
- return hypothetical;
- }
-
- @Override
- public String getElementId() {
- return this.idSpecies;
- }
-
- @Override
- public void setElementId(String id) {
- if (this.idSpecies.equals(id) || this.idSpecies.equals("")) {
- this.idSpecies = id;
- } else if (!id.equals("")) {
- throw new InvalidArgumentException("Cannot change identifier of the species in the runtime. OLD: " + this.idSpecies + ", NEW: " + id);
- } else {
- this.idSpecies = id;
- }
- }
-
- /**
- * @return the initialAmount
- * @see #initialAmount
- */
- public Integer getInitialAmount() {
- return initialAmount;
- }
-
- /**
- * @param initialAmount
- * the initialAmount to set
- * @see #initialAmount
- */
- public void setInitialAmount(Integer initialAmount) {
- this.initialAmount = initialAmount;
- }
-
- /**
- * @return the charge
- * @see #charge
- */
- public Integer getCharge() {
- return charge;
- }
-
- /**
- * @param charge
- * the charge to set
- * @see #charge
- */
- public void setCharge(Integer charge) {
- this.charge = charge;
- }
-
- /**
- * @return the onlySubstanceUnits
- * @see #onlySubstanceUnits
- */
- public Boolean getOnlySubstanceUnits() {
- return onlySubstanceUnits;
- }
-
- /**
- * @param onlySubstanceUnits
- * the onlySubstanceUnits to set
- * @see #onlySubstanceUnits
- */
- public void setOnlySubstanceUnits(Boolean onlySubstanceUnits) {
- this.onlySubstanceUnits = onlySubstanceUnits;
- }
-
- /**
- * @return the initialConcentration
- * @see #initialConcentration
- */
- public Integer getInitialConcentration() {
- return initialConcentration;
- }
-
- /**
- * @param initialConcentration
- * the initialConcentration to set
- * @see #initialConcentration
- */
- public void setInitialConcentration(Integer initialConcentration) {
- this.initialConcentration = initialConcentration;
- }
-
- /**
- * @return the hypothetical
- * @see #hypothetical
- */
- public Boolean getHypothetical() {
- return hypothetical;
- }
-
- /**
- * @param hypothetical
- * the hypothetical to set
- * @see #hypothetical
- */
- public void setHypothetical(Boolean hypothetical) {
- this.hypothetical = hypothetical;
- }
-
- /**
- * @return the onlySubstanceUnits
- * @see #onlySubstanceUnits
- */
- public Boolean hasOnlySubstanceUnits() {
- return onlySubstanceUnits;
- }
-
- /**
- * @return the positionToCompartment
- * @see #positionToCompartment
- */
- public PositionToCompartment getPositionToCompartment() {
- return positionToCompartment;
- }
-
- /**
- * @param positionToCompartment
- * the positionToCompartment to set
- * @see #positionToCompartment
- */
- public void setPositionToCompartment(PositionToCompartment positionToCompartment) {
- this.positionToCompartment = positionToCompartment;
- }
-
- /**
- * @return the homodimer
- * @see #homodimer
- */
- public int getHomodimer() {
- return homodimer;
- }
-
- /**
- * @param homodimer
- * the homodimer to set
- * @see #homodimer
- */
- public void setHomodimer(int homodimer) {
- this.homodimer = homodimer;
- }
-
- @Override
- public T createModelElement(String aliasId) {
- throw new NotImplementedException("" + this.getClass());
- }
-
- @Override
- protected void setModelObjectFields(T result) {
- super.setModelObjectFields(result);
- result.setInitialAmount(initialAmount);
- result.setCharge(charge);
- result.setInitialConcentration(initialConcentration);
- result.setOnlySubstanceUnits(onlySubstanceUnits);
- result.setHomodimer(homodimer);
- result.setPositionToCompartment(positionToCompartment);
- result.setHypothetical(hypothetical);
- }
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Default class logger.
+ */
+ private static Logger logger = Logger.getLogger(CellDesignerSpecies.class.getName());
+
+ /**
+ * Identifier of the species. It must be unique within the model.
+ */
+ private String idSpecies;
+
+ /**
+ * Initial amount of species.
+ */
+ private Double initialAmount = null;
+
+ /**
+ * Charge of the species.
+ */
+ private Integer charge = null;
+
+ /**
+ * Initial concentration of species.
+ */
+ private Double initialConcentration = null;
+
+ /**
+ * Is only substance units allowed.
+ */
+ private Boolean onlySubstanceUnits = null;
+
+ /**
+ * How many dimers are in this species.
+ */
+ private int homodimer = 1;
+
+ /**
+ * Position on the compartment.
+ */
+ private PositionToCompartment positionToCompartment = null;
+
+ /**
+ * Is species hypothetical.
+ */
+ private Boolean hypothetical = null;
+
+ private SbmlUnitType substanceUnits;
+
+ private Boolean boundaryCondition;
+
+ private Boolean constant;
+
+ /**
+ * Set hypothetical flag from text input.
+ *
+ * @param text
+ * string with true/false value that determines hypothetical state.
+ * @see #hypothetical
+ */
+ public void setHypothetical(String text) {
+ hypothetical = text.equals("true");
+ }
+
+ /**
+ * Constructor that copies the data from species given in the argument.
+ *
+ * @param species
+ * parent species from which we want to copy data
+ */
+ public CellDesignerSpecies(CellDesignerSpecies<?> species) {
+ super(species);
+ this.hypothetical = species.hypothetical;
+ this.idSpecies = species.idSpecies;
+ this.positionToCompartment = species.positionToCompartment;
+ this.initialAmount = species.initialAmount;
+ this.charge = species.charge;
+ this.initialConcentration = species.initialConcentration;
+ this.onlySubstanceUnits = species.onlySubstanceUnits;
+ this.homodimer = species.homodimer;
+ this.constant = species.constant;
+ this.substanceUnits = species.substanceUnits;
+ this.boundaryCondition = species.boundaryCondition;
+ }
+
+ /**
+ * Default constructor.
+ */
+ public CellDesignerSpecies() {
+ super();
+ idSpecies = "";
+ }
+
+ /**
+ * Default constructor with species identifier as a parameter.
+ *
+ * @param id
+ * species identifier
+ */
+ public CellDesignerSpecies(String id) {
+ this();
+ this.idSpecies = id;
+ this.setName(id);
+ }
+
+ @Override
+ public CellDesignerSpecies<T> copy() {
+ CellDesignerSpecies<T> result = new CellDesignerSpecies<T>(this);
+
+ result.idSpecies = idSpecies;
+ result.setNotes(getNotes());
+ result.setHypothetical(hypothetical);
+ // correct this
+
+ result.setParent(getParent());
+
+ return result;
+ }
+
+ /**
+ * Updates species with the value from the species given in the parameter.
+ *
+ * @param species
+ * object from which we are updating information
+ */
+ public void update(CellDesignerSpecies<?> species) {
+ if (getName() == null || getName().equals("")) {
+ setName(species.getName());
+ } else if (!getName().trim().equals(species.getName().trim())) {
+ String id = species.getElementId();
+ if (id == null || id.equals("")) {
+ id = getElementId();
+ }
+ logger.warn(
+ "Two different names in species with id =" + id + ": \"" + species.getName() + "\", \"" + getName() + "\"");
+ setName(species.getName());
+ }
+ if (idSpecies == null || idSpecies.equals("")) {
+ setElementId(species.getElementId());
+ }
+ for (MiriamData md : species.getMiriamData()) {
+ if (!getMiriamData().contains(md)) {
+ addMiriamData(new MiriamData(md));
+ }
+ }
+ if (this.getNotes() == null || this.getNotes().trim().equals("")) {
+ setNotes(species.getNotes());
+ } else if (species.getNotes() != null && !species.getNotes().trim().equals("")
+ && !this.getNotes().equals(species.getNotes())) {
+ String string1 = this.getNotes();
+
+ String string2 = species.getNotes();
+
+ string1 = string1.trim();
+ string2 = string2.trim();
+ if (string2.toLowerCase().contains(string1.toLowerCase())) {
+ setNotes(species.getNotes());
+ } else if (!string1.toLowerCase().contains(string2.toLowerCase())) {
+ // insert new information
+ setNotes(string2 + getNotes());
+ }
+ }
+
+ if (getParent() == null) {
+ setParent(species.getParent());
+ }
+
+ if (species.getHypothetical() != null) {
+ setHypothetical(species.getHypothetical());
+ }
+
+ if (getSymbol() != null && !getSymbol().equals("")) {
+ if (species.getSymbol() != null && !species.getSymbol().equals("")) {
+ if (!species.getSymbol().equals(getSymbol())) {
+ logger.warn("Different symbol names: " + species.getSymbol() + ", " + getSymbol() + ". Ignoring...");
+ }
+ }
+ } else {
+ setSymbol(species.getSymbol());
+ }
+
+ if (getFullName() != null && !getFullName().equals("")) {
+ if (species.getFullName() != null && !species.getFullName().equals("")) {
+ if (!species.getFullName().equals(getFullName())) {
+ logger.warn("Different symbol names: " + species.getFullName() + ", " + getFullName() + ". Ignoring...");
+ }
+ }
+ } else {
+ setFullName(species.getFullName());
+ }
+
+ for (String string : species.getSynonyms()) {
+ if (!getSynonyms().contains(string)) {
+ getSynonyms().add(string);
+ }
+ }
+
+ for (String string : species.getFormerSymbols()) {
+ if (!getFormerSymbols().contains(string)) {
+ getFormerSymbols().add(string);
+ }
+ }
+ if (species.getHomodimer() != 1) {
+ setHomodimer(species.getHomodimer());
+ }
+ }
+
+ /**
+ * Sets initial amount from text.
+ *
+ * @param text
+ * initial amount in string format
+ * @see #initialAmount
+ */
+
+ public void setInitialAmount(String text) {
+ if (text != null && !text.trim().equals("")) {
+ try {
+ initialAmount = Double.parseDouble(text);
+ } catch (NumberFormatException e) {
+ throw new InvalidArgumentException("Invalid species amount: " + text, e);
+ }
+ } else {
+ initialAmount = null;
+ }
+
+ }
+
+ /**
+ * Sets charge from text.
+ *
+ * @param text
+ * charge in string format
+ * @see #charge
+ */
+ public void setCharge(String text) {
+ if (text != null && !text.trim().equals("")) {
+ try {
+ charge = Integer.parseInt(text);
+ } catch (NumberFormatException e) {
+ throw new InvalidArgumentException("Invalid species charge: " + text, e);
+ }
+ } else {
+ charge = null;
+ }
+
+ }
+
+ /**
+ * Sets OnlySubstanceUnits amount from text.
+ *
+ * @param text
+ * OnlySubstanceUnits in string format
+ * @see #onlySubstanceUnits
+ */
+ public void setOnlySubstanceUnits(String text) {
+ onlySubstanceUnits = textToBoolean(text, "Invalid species value for only substance unit boolean: " + text);
+ }
+
+ /**
+ * Sets initial concentration amount from text.
+ *
+ * @param text
+ * initial concentration in string format
+ * @see #initialConcentration
+ */
+ public void setInitialConcentration(String text) {
+ if (text != null && !text.trim().equals("")) {
+ try {
+ initialConcentration = Double.parseDouble(text);
+ } catch (NumberFormatException e) {
+ throw new InvalidArgumentException("Invalid species initial concentration: " + text, e);
+ }
+ } else {
+ initialConcentration = null;
+ }
+ }
+
+ /**
+ * Is species hypothetical or not.
+ *
+ * @return <code>true</code> if species is hypothetical, <code>false</code>
+ * otherwise
+ */
+ public boolean isHypothetical() {
+ if (hypothetical == null) {
+ return false;
+ }
+ return hypothetical;
+ }
+
+ @Override
+ public String getElementId() {
+ return this.idSpecies;
+ }
+
+ @Override
+ public void setElementId(String id) {
+ if (this.idSpecies.equals(id) || this.idSpecies.equals("")) {
+ this.idSpecies = id;
+ } else if (!id.equals("")) {
+ throw new InvalidArgumentException(
+ "Cannot change identifier of the species in the runtime. OLD: " + this.idSpecies + ", NEW: " + id);
+ } else {
+ this.idSpecies = id;
+ }
+ }
+
+ /**
+ * @return the initialAmount
+ * @see #initialAmount
+ */
+ public Double getInitialAmount() {
+ return initialAmount;
+ }
+
+ /**
+ * @param initialAmount
+ * the initialAmount to set
+ * @see #initialAmount
+ */
+ public void setInitialAmount(Double initialAmount) {
+ this.initialAmount = initialAmount;
+ }
+
+ /**
+ * @return the charge
+ * @see #charge
+ */
+ public Integer getCharge() {
+ return charge;
+ }
+
+ /**
+ * @param charge
+ * the charge to set
+ * @see #charge
+ */
+ public void setCharge(Integer charge) {
+ this.charge = charge;
+ }
+
+ /**
+ * @return the onlySubstanceUnits
+ * @see #onlySubstanceUnits
+ */
+ public Boolean getOnlySubstanceUnits() {
+ return onlySubstanceUnits;
+ }
+
+ /**
+ * @param onlySubstanceUnits
+ * the onlySubstanceUnits to set
+ * @see #onlySubstanceUnits
+ */
+ public void setOnlySubstanceUnits(Boolean onlySubstanceUnits) {
+ this.onlySubstanceUnits = onlySubstanceUnits;
+ }
+
+ /**
+ * @return the initialConcentration
+ * @see #initialConcentration
+ */
+ public Double getInitialConcentration() {
+ return initialConcentration;
+ }
+
+ /**
+ * @param initialConcentration
+ * the initialConcentration to set
+ * @see #initialConcentration
+ */
+ public void setInitialConcentration(Double initialConcentration) {
+ this.initialConcentration = initialConcentration;
+ }
+
+ /**
+ * @return the hypothetical
+ * @see #hypothetical
+ */
+ public Boolean getHypothetical() {
+ return hypothetical;
+ }
+
+ /**
+ * @param hypothetical
+ * the hypothetical to set
+ * @see #hypothetical
+ */
+ public void setHypothetical(Boolean hypothetical) {
+ this.hypothetical = hypothetical;
+ }
+
+ /**
+ * @return the onlySubstanceUnits
+ * @see #onlySubstanceUnits
+ */
+ public Boolean hasOnlySubstanceUnits() {
+ return onlySubstanceUnits;
+ }
+
+ /**
+ * @return the positionToCompartment
+ * @see #positionToCompartment
+ */
+ public PositionToCompartment getPositionToCompartment() {
+ return positionToCompartment;
+ }
+
+ /**
+ * @param positionToCompartment
+ * the positionToCompartment to set
+ * @see #positionToCompartment
+ */
+ public void setPositionToCompartment(PositionToCompartment positionToCompartment) {
+ this.positionToCompartment = positionToCompartment;
+ }
+
+ /**
+ * @return the homodimer
+ * @see #homodimer
+ */
+ public int getHomodimer() {
+ return homodimer;
+ }
+
+ /**
+ * @param homodimer
+ * the homodimer to set
+ * @see #homodimer
+ */
+ public void setHomodimer(int homodimer) {
+ this.homodimer = homodimer;
+ }
+
+ @Override
+ public T createModelElement(String aliasId) {
+ throw new NotImplementedException("" + this.getClass());
+ }
+
+ @Override
+ protected void setModelObjectFields(T result) {
+ super.setModelObjectFields(result);
+ result.setInitialAmount(initialAmount);
+ result.setCharge(charge);
+ result.setInitialConcentration(initialConcentration);
+ result.setOnlySubstanceUnits(onlySubstanceUnits);
+ result.setConstant(constant);
+ result.setBoundaryCondition(boundaryCondition);
+ result.setSubstanceUnits(substanceUnits);
+ result.setHomodimer(homodimer);
+ result.setPositionToCompartment(positionToCompartment);
+ result.setHypothetical(hypothetical);
+ }
+
+ public void setSubstanceUnits(SbmlUnitType substanceUnits) {
+ this.substanceUnits = substanceUnits;
+ }
+
+ public SbmlUnitType getSubstanceUnit() {
+ return this.substanceUnits;
+ }
+
+ public Boolean isBoundaryCondition() {
+ return boundaryCondition;
+ }
+
+ public Boolean isConstant() {
+ return constant;
+ }
+
+ public void setBoundaryCondition(String text) {
+ boundaryCondition = textToBoolean(text, "Invalid species value for only substance unit boolean: " + text);
+ }
+
+ private Boolean textToBoolean(String text, String errorMessage) {
+ Boolean result;
+ if (text != null && !text.trim().equals("")) {
+ if (text.equalsIgnoreCase("TRUE")) {
+ result = true;
+ } else if (text.equalsIgnoreCase("FALSE")) {
+ result = false;
+ } else {
+ throw new InvalidArgumentException(errorMessage);
+ }
+ } else {
+ result = null;
+ }
+ return result;
+ }
+
+ public void setConstant(String text) {
+ constant = textToBoolean(text, "Invalid species value for only constant boolean: " + text);
+ }
+
+ public void setBoundaryCondition(Boolean boundaryCondition) {
+ this.boundaryCondition = boundaryCondition;
+ }
+
+ public void setConstant(Boolean constant) {
+ this.constant = constant;
+ }
}
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/ComplexParserTests.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/ComplexParserTests.java
index b2686560126584ec847aa05c4c912b2b9e7b7c35..010a5dc8da7033b0052d0f34d2a4790992ed12e9 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/ComplexParserTests.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/ComplexParserTests.java
@@ -18,9 +18,11 @@ import org.junit.After;
import org.junit.Before;
import org.junit.Test;
+import lcsb.mapviewer.common.Configuration;
import lcsb.mapviewer.converter.ConverterParams;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamType;
+import lcsb.mapviewer.model.map.kinetics.SbmlUnitType;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.model.ModelComparator;
import lcsb.mapviewer.model.map.model.ModelFullIndexed;
@@ -75,6 +77,23 @@ public class ComplexParserTests extends CellDesignerTestFunctions {
}
}
+ @Test
+ public void testParseElementKinetics() throws Exception {
+ try {
+ Model model = getModelForFile("testFiles/elements_with_kinetic_data.xml");
+
+ GenericProtein protein1 = model.getElementByElementId("sa1");
+ assertEquals(2.5, protein1.getInitialAmount(), Configuration.EPSILON);
+ assertTrue("hasOnlySubstance property is not parsed properly", protein1.hasOnlySubstanceUnits());
+ assertTrue("boundaryCondition property is not parsed properly", protein1.isBoundaryCondition());
+ assertTrue("constant property is not parsed properly", protein1.isConstant());
+ assertEquals(SbmlUnitType.GRAM, protein1.getSubstanceUnits());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
@Test
public void testParseUnits() throws Exception {
try {
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/species/SpeciesSbmlParserTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/species/SpeciesSbmlParserTest.java
index 24833a18ae2f1cb965a525d081cac0e87d101517..01d8192151ac435f98f1becce3118adca2e63db8 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/species/SpeciesSbmlParserTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/species/SpeciesSbmlParserTest.java
@@ -20,6 +20,7 @@ import org.w3c.dom.Document;
import org.w3c.dom.NodeList;
import org.xml.sax.InputSource;
+import lcsb.mapviewer.common.Configuration;
import lcsb.mapviewer.common.Pair;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
@@ -43,1052 +44,1095 @@ import lcsb.mapviewer.converter.model.celldesigner.structure.fields.CellDesigner
import lcsb.mapviewer.converter.model.celldesigner.structure.fields.CellDesignerModificationResidue;
import lcsb.mapviewer.converter.model.celldesigner.structure.fields.CellDesignerRnaRegion;
import lcsb.mapviewer.converter.model.celldesigner.structure.fields.SpeciesState;
+import lcsb.mapviewer.model.map.kinetics.SbmlUnitType;
import lcsb.mapviewer.model.map.species.Gene;
import lcsb.mapviewer.model.map.species.GenericProtein;
import lcsb.mapviewer.model.map.species.Species;
public class SpeciesSbmlParserTest extends CellDesignerTestFunctions {
- @SuppressWarnings("unused")
- private Logger logger = Logger.getLogger(SpeciesSbmlParserTest.class.getName());
-
- SpeciesSbmlParser parser;
-
- String testDirectory = "testFiles" + System.getProperty("file.separator") + "xmlNodeTestExamples"
- + System.getProperty("file.separator");
- String testGeneFile = "sbml_gene.xml";
- String testDegradedFile = "sbml_degraded.xml";
- String testDrugFile = "sbml_drug.xml";
- String testIonFile = "sbml_ion.xml";
- String testPhenotypeFile = "sbml_phenotype.xml";
- String testProteinFile = "sbml_protein.xml";
- String testRnaFile = "sbml_rna.xml";
- String testSimpleMoleculeFile = "sbml_simple_molecule.xml";
- String testUnknownFile = "sbml_unknown.xml";
-
- CellDesignerElementCollection elements;
-
- int idCounter = 0;
-
- @Before
- public void setUp() throws Exception {
- elements = new CellDesignerElementCollection();
- parser = new SpeciesSbmlParser(elements);
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testParseXmlSpeciesAntisenseRna() throws Exception {
- try {
- String xmlString = readFile(testDirectory + "sbml_antisense_rna.xml");
- Pair<String, ? extends CellDesignerSpecies<?>> result = parser.parseXmlElement(xmlString);
- CellDesignerAntisenseRna species = (CellDesignerAntisenseRna) result.getRight();
- assertEquals("s2", species.getElementId());
- assertEquals("s3", species.getName());
- assertEquals(new Integer(2), species.getInitialAmount());
- assertEquals(Boolean.TRUE, species.hasOnlySubstanceUnits());
- assertEquals(new Integer(0), species.getCharge());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testToXmlAntisenseRna() throws Exception {
- try {
- String xmlString = readFile(testDirectory + "sbml_antisense_rna.xml");
- Pair<String, ? extends CellDesignerSpecies<?>> result = parser.parseXmlElement(xmlString);
- CellDesignerAntisenseRna species = (CellDesignerAntisenseRna) result.getRight();
-
- String transformedXml = parser.toXml(species.createModelElement());
- assertNotNull(transformedXml);
- DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
- DocumentBuilder builder = factory.newDocumentBuilder();
- InputSource is = new InputSource(new StringReader(transformedXml));
- Document doc = builder.parse(is);
- NodeList root = doc.getChildNodes();
- assertEquals("species", root.item(0).getNodeName());
-
- Pair<String, ? extends CellDesignerSpecies<?>> result2 = parser.parseXmlElement(parser.toXml(species.createModelElement()));
- CellDesignerAntisenseRna species2 = (CellDesignerAntisenseRna) result2.getRight();
-
- assertEquals(species.getName(), species2.getName());
- assertEquals(species.getParent(), species2.getParent());
- assertEquals(species.getInitialAmount(), species2.getInitialAmount());
- assertEquals(species.hasOnlySubstanceUnits(), species2.hasOnlySubstanceUnits());
- assertEquals(species.getCharge(), species2.getCharge());
- assertEquals(species.getPositionToCompartment(), species2.getPositionToCompartment());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testParseXmlSpeciesComplex() throws Exception {
- try {
- String xmlString = readFile(testDirectory + "sbml_complex.xml");
- Pair<String, ? extends CellDesignerSpecies<?>> result = parser.parseXmlElement(xmlString);
- CellDesignerComplexSpecies species = (CellDesignerComplexSpecies) result.getRight();
- assertNotNull(species);
- assertEquals("s6549", species.getElementId());
- assertEquals("LC3-II", species.getName());
- assertEquals(new Integer(0), species.getInitialAmount());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testToXmlComplex() throws Exception {
- try {
- String xmlString = readFile(testDirectory + "sbml_complex.xml");
- Pair<String, ? extends CellDesignerSpecies<?>> result = parser.parseXmlElement(xmlString);
- CellDesignerComplexSpecies species = (CellDesignerComplexSpecies) result.getRight();
-
- String transformedXml = parser.toXml(species.createModelElement());
- assertNotNull(transformedXml);
- DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
- DocumentBuilder builder = factory.newDocumentBuilder();
- InputSource is = new InputSource(new StringReader(transformedXml));
- Document doc = builder.parse(is);
- NodeList root = doc.getChildNodes();
- assertEquals("species", root.item(0).getNodeName());
-
- Pair<String, ? extends CellDesignerSpecies<?>> result2 = parser.parseXmlElement(parser.toXml(species.createModelElement()));
- CellDesignerComplexSpecies species2 = (CellDesignerComplexSpecies) result2.getRight();
-
- assertNotNull(species2);
- assertEquals(species.getName(), species2.getName());
- assertEquals(species.getParent(), species2.getParent());
- assertEquals(species.getInitialAmount(), species2.getInitialAmount());
- assertEquals(species.hasOnlySubstanceUnits(), species2.hasOnlySubstanceUnits());
- assertEquals(species.getCharge(), species2.getCharge());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testParseXmlSpeciesDegraded() throws Exception {
- try {
- String xmlString = readFile(testDirectory + testDegradedFile);
- Pair<String, ? extends CellDesignerSpecies<?>> result = parser.parseXmlElement(xmlString);
- CellDesignerDegraded species = (CellDesignerDegraded) result.getRight();
- assertNotNull(species);
- assertEquals("s1275", species.getElementId());
- assertEquals("s1275", species.getName());
- assertEquals(new Integer(0), species.getInitialAmount());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testToXmlDegraded() throws Exception {
- try {
- String xmlString = readFile(testDirectory + testDegradedFile);
- Pair<String, ? extends CellDesignerSpecies<?>> result = parser.parseXmlElement(xmlString);
- CellDesignerDegraded species = (CellDesignerDegraded) result.getRight();
-
- String transformedXml = parser.toXml(species.createModelElement());
- assertNotNull(transformedXml);
- DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
- DocumentBuilder builder = factory.newDocumentBuilder();
- InputSource is = new InputSource(new StringReader(transformedXml));
- Document doc = builder.parse(is);
- NodeList root = doc.getChildNodes();
- assertEquals("species", root.item(0).getNodeName());
-
- Pair<String, ? extends CellDesignerSpecies<?>> result2 = parser.parseXmlElement(parser.toXml(species.createModelElement()));
- CellDesignerDegraded species2 = (CellDesignerDegraded) result2.getRight();
-
- assertNotNull(species2);
- assertEquals(species.getName(), species2.getName());
- assertEquals(species.getParent(), species2.getParent());
- assertEquals(species.getInitialAmount(), species2.getInitialAmount());
- assertEquals(species.hasOnlySubstanceUnits(), species2.hasOnlySubstanceUnits());
- assertEquals(species.getCharge(), species2.getCharge());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testParseXmlSpeciesDrug() throws Exception {
- try {
- String xmlString = readFile(testDirectory + testDrugFile);
- Pair<String, ? extends CellDesignerSpecies<?>> result = parser.parseXmlElement(xmlString);
- CellDesignerDrug species = (CellDesignerDrug) result.getRight();
- assertEquals("s6104", species.getElementId());
- assertEquals("geldanamycin", species.getName());
- assertEquals(new Integer(0), species.getCharge());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testToXmlDrug() throws Exception {
- try {
- String xmlString = readFile(testDirectory + testDrugFile);
- Pair<String, ? extends CellDesignerSpecies<?>> result = parser.parseXmlElement(xmlString);
- CellDesignerDrug species = (CellDesignerDrug) result.getRight();
-
- String transformedXml = parser.toXml(species.createModelElement());
- assertNotNull(transformedXml);
- DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
- DocumentBuilder builder = factory.newDocumentBuilder();
- InputSource is = new InputSource(new StringReader(transformedXml));
- Document doc = builder.parse(is);
- NodeList root = doc.getChildNodes();
- assertEquals("species", root.item(0).getNodeName());
-
- Pair<String, ? extends CellDesignerSpecies<?>> result2 = parser.parseXmlElement(parser.toXml(species.createModelElement()));
- CellDesignerDrug species2 = (CellDesignerDrug) result2.getRight();
-
- assertNotNull(species2);
- assertEquals(species.getName(), species2.getName());
- assertEquals(species.getParent(), species2.getParent());
- assertEquals(species.getInitialAmount(), species2.getInitialAmount());
- assertEquals(species.hasOnlySubstanceUnits(), species2.hasOnlySubstanceUnits());
- assertEquals(species.getCharge(), species2.getCharge());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testParseXmlSpeciesGene() throws Exception {
- try {
- String xmlString = readFile(testDirectory + testGeneFile);
- Pair<String, ? extends CellDesignerSpecies<?>> result = parser.parseXmlElement(xmlString);
- CellDesignerGene species = (CellDesignerGene) result.getRight();
-
- assertEquals("s5916", species.getElementId());
- assertEquals("Ptgr1", species.getName());
- assertEquals(new Integer(0), species.getCharge());
- assertEquals(new Integer(0), species.getInitialAmount());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testParseXmlSpeciesGeneWithModelUpdate() throws Exception {
- try {
- CellDesignerSpecies<?> gene = new CellDesignerGene();
- gene.setElementId("s5916");
- InternalModelSpeciesData modelData = new InternalModelSpeciesData();
- modelData.updateSpecies(gene, "");
-
- SpeciesSbmlParser complexParser = new SpeciesSbmlParser(elements);
- CellDesignerGene oldGene = new CellDesignerGene();
- oldGene.setElementId("s5916");
- oldGene.setName("Ptgr1");
- modelData.updateSpecies(oldGene, "gn95");
-
- String xmlString = readFile(testDirectory + testGeneFile);
- Pair<String, ? extends CellDesignerSpecies<?>> result = complexParser.parseXmlElement(xmlString);
- CellDesignerGene species = (CellDesignerGene) result.getRight();
- modelData.updateSpecies(species, result.getLeft());
-
- assertEquals("s5916", species.getElementId());
- assertEquals("Ptgr1", species.getName());
- assertTrue(species.getNotes().contains("prostaglandin reductase 1"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testToXmlGene() throws Exception {
- try {
- String xmlString = readFile(testDirectory + testGeneFile);
- Pair<String, ? extends CellDesignerSpecies<?>> result = parser.parseXmlElement(xmlString);
- CellDesignerGene species = (CellDesignerGene) result.getRight();
-
- String transformedXml = parser.toXml(species.createModelElement());
- assertNotNull(transformedXml);
- DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
- DocumentBuilder builder = factory.newDocumentBuilder();
- InputSource is = new InputSource(new StringReader(transformedXml));
- Document doc = builder.parse(is);
- NodeList root = doc.getChildNodes();
- assertEquals("species", root.item(0).getNodeName());
-
- Pair<String, ? extends CellDesignerSpecies<?>> result2 = parser.parseXmlElement(parser.toXml(species.createModelElement()));
- CellDesignerGene species2 = (CellDesignerGene) result2.getRight();
-
- assertNotNull(species2);
- assertEquals(species.getName(), species2.getName());
- assertEquals(species.getParent(), species2.getParent());
- assertEquals(species.getInitialAmount(), species2.getInitialAmount());
- assertEquals(species.hasOnlySubstanceUnits(), species2.hasOnlySubstanceUnits());
- assertEquals(species.getCharge(), species2.getCharge());
- assertTrue(species2.getNotes().trim().contains(species.getNotes().trim()));
- assertEquals(species.getMiriamData().size(), species2.getMiriamData().size());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testParseXmlSpeciesIon() throws Exception {
- try {
- String xmlString = readFile(testDirectory + testIonFile);
- Pair<String, ? extends CellDesignerSpecies<?>> result = parser.parseXmlElement(xmlString);
- CellDesignerIon species = (CellDesignerIon) result.getRight();
-
- assertEquals("s6029", species.getElementId());
- assertEquals("Pi", species.getName());
- assertEquals(new Integer(0), species.getCharge());
- assertEquals(new Integer(0), species.getInitialConcentration());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testToXmlIon() throws Exception {
- try {
- String xmlString = readFile(testDirectory + testIonFile);
- Pair<String, ? extends CellDesignerSpecies<?>> result = parser.parseXmlElement(xmlString);
- CellDesignerIon species = (CellDesignerIon) result.getRight();
-
- String transformedXml = parser.toXml(species.createModelElement());
- assertNotNull(transformedXml);
- DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
- DocumentBuilder builder = factory.newDocumentBuilder();
- InputSource is = new InputSource(new StringReader(transformedXml));
- Document doc = builder.parse(is);
- NodeList root = doc.getChildNodes();
- assertEquals("species", root.item(0).getNodeName());
-
- Pair<String, ? extends CellDesignerSpecies<?>> result2 = parser.parseXmlElement(xmlString);
- CellDesignerIon species2 = (CellDesignerIon) result2.getRight();
-
- assertNotNull(species2);
- assertEquals(species.getElementId(), species2.getElementId());
- assertEquals(species.getName(), species2.getName());
- assertEquals(species.getParent(), species2.getParent());
- assertEquals(species.getInitialAmount(), species2.getInitialAmount());
- assertEquals(species.hasOnlySubstanceUnits(), species2.hasOnlySubstanceUnits());
- assertEquals(species.getCharge(), species2.getCharge());
- assertEquals(species.getInitialConcentration(), species2.getInitialConcentration());
- assertEquals(species.getNotes().trim(), species2.getNotes().trim());
- assertEquals(species.getMiriamData().size(), species2.getMiriamData().size());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testParseXmlSpeciesPhenotype() throws Exception {
- try {
- String xmlString = readFile(testDirectory + testPhenotypeFile);
- Pair<String, ? extends CellDesignerSpecies<?>> result = parser.parseXmlElement(xmlString);
- CellDesignerPhenotype species = (CellDesignerPhenotype) result.getRight();
-
- assertEquals("s5462", species.getElementId());
- assertEquals("Neuronal damage and death", species.getName());
- assertEquals(new Integer(0), species.getInitialAmount());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testToXmlPhenotype() throws Exception {
- try {
- String xmlString = readFile(testDirectory + testPhenotypeFile);
- Pair<String, ? extends CellDesignerSpecies<?>> result = parser.parseXmlElement(xmlString);
- CellDesignerPhenotype species = (CellDesignerPhenotype) result.getRight();
-
- String transformedXml = parser.toXml(species.createModelElement());
- assertNotNull(transformedXml);
- DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
- DocumentBuilder builder = factory.newDocumentBuilder();
- InputSource is = new InputSource(new StringReader(transformedXml));
- Document doc = builder.parse(is);
- NodeList root = doc.getChildNodes();
- assertEquals("species", root.item(0).getNodeName());
-
- Pair<String, ? extends CellDesignerSpecies<?>> result2 = parser.parseXmlElement(parser.toXml(species.createModelElement()));
- CellDesignerPhenotype species2 = (CellDesignerPhenotype) result2.getRight();
-
- assertNotNull(species2);
- assertEquals(species.getName(), species2.getName());
- assertEquals(species.getParent(), species2.getParent());
- assertEquals(species.getInitialAmount(), species2.getInitialAmount());
- assertEquals(species.hasOnlySubstanceUnits(), species2.hasOnlySubstanceUnits());
- assertEquals(species.getCharge(), species2.getCharge());
- assertEquals(species.getInitialConcentration(), species2.getInitialConcentration());
- assertEquals(species.getNotes(), species2.getNotes());
- assertEquals(species.getMiriamData().size(), species2.getMiriamData().size());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testParseXmlSpeciesProtein() throws Exception {
- try {
- String xmlString = readFile(testDirectory + testProteinFile);
- Pair<String, ? extends CellDesignerSpecies<?>> result = parser.parseXmlElement(xmlString);
- CellDesignerProtein<?> species = (CellDesignerProtein<?>) result.getRight();
-
- assertEquals("s5456", species.getElementId());
- assertEquals("PTPRC", species.getName());
- assertEquals(new Integer(0), species.getInitialAmount());
- assertEquals(new Integer(0), species.getCharge());
- assertTrue(species.getNotes().contains("protein tyrosine phosphatase, receptor type, C"));
- assertNull(species.getStructuralState());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testToXmlProtein() throws Exception {
- try {
- String xmlString = readFile(testDirectory + testProteinFile);
- Pair<String, ? extends CellDesignerSpecies<?>> result = parser.parseXmlElement(xmlString);
- CellDesignerGenericProtein species = new CellDesignerGenericProtein(result.getRight());
-
- String transformedXml = parser.toXml(species.createModelElement("" + idCounter++));
- assertNotNull(transformedXml);
- DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
- DocumentBuilder builder = factory.newDocumentBuilder();
- InputSource is = new InputSource(new StringReader(transformedXml));
- Document doc = builder.parse(is);
- NodeList root = doc.getChildNodes();
- assertEquals("species", root.item(0).getNodeName());
-
- Pair<String, ? extends CellDesignerSpecies<?>> result2 = parser.parseXmlElement(parser.toXml(species.createModelElement("" + idCounter++)));
- CellDesignerProtein<?> species2 = (CellDesignerProtein<?>) result2.getRight();
-
- assertNotNull(species2);
- assertEquals(species.getName(), species2.getName());
- assertEquals(species.getParent(), species2.getParent());
- assertEquals(species.getInitialAmount(), species2.getInitialAmount());
- assertEquals(species.hasOnlySubstanceUnits(), species2.hasOnlySubstanceUnits());
- assertEquals(species.getCharge(), species2.getCharge());
- assertEquals(species.getInitialConcentration(), species2.getInitialConcentration());
- assertTrue(species2.getNotes().contains(species.getNotes()));
- assertEquals(species.getMiriamData().size(), species2.getMiriamData().size());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testParseXmlSpeciesRna() throws Exception {
- try {
- String xmlString = readFile(testDirectory + testRnaFile);
- Pair<String, ? extends CellDesignerSpecies<?>> result = parser.parseXmlElement(xmlString);
- CellDesignerRna species = (CellDesignerRna) result.getRight();
-
- assertEquals("s5914", species.getElementId());
- assertEquals("Fmo3", species.getName());
- assertEquals(new Integer(0), species.getInitialAmount());
- assertEquals(new Integer(0), species.getCharge());
- assertTrue(species.getNotes().contains("Dimethylaniline monooxygenase [N-oxide-forming] 3"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testToXmlRna() throws Exception {
- try {
- String xmlString = readFile(testDirectory + testRnaFile);
- Pair<String, ? extends CellDesignerSpecies<?>> result = parser.parseXmlElement(xmlString);
- CellDesignerRna species = (CellDesignerRna) result.getRight();
-
- String transformedXml = parser.toXml(species.createModelElement());
- assertNotNull(transformedXml);
- DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
- DocumentBuilder builder = factory.newDocumentBuilder();
- InputSource is = new InputSource(new StringReader(transformedXml));
- Document doc = builder.parse(is);
- NodeList root = doc.getChildNodes();
- assertEquals("species", root.item(0).getNodeName());
-
- Pair<String, ? extends CellDesignerSpecies<?>> result2 = parser.parseXmlElement(parser.toXml(species.createModelElement()));
- CellDesignerRna species2 = (CellDesignerRna) result2.getRight();
-
- assertNotNull(species2);
- assertEquals(species.getName(), species2.getName());
- assertEquals(species.getParent(), species2.getParent());
- assertEquals(species.getInitialAmount(), species2.getInitialAmount());
- assertEquals(species.hasOnlySubstanceUnits(), species2.hasOnlySubstanceUnits());
- assertEquals(species.getCharge(), species2.getCharge());
- assertEquals(species.getInitialConcentration(), species2.getInitialConcentration());
- assertTrue(species2.getNotes().trim().contains(species.getNotes().trim()));
- assertEquals(species.getMiriamData().size(), species2.getMiriamData().size());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testParseXmlSpeciesSimpleMolecule() throws Exception {
- try {
- String xmlString = readFile(testDirectory + testSimpleMoleculeFile);
- Pair<String, ? extends CellDesignerSpecies<?>> result = parser.parseXmlElement(xmlString);
- CellDesignerSimpleMolecule species = (CellDesignerSimpleMolecule) result.getRight();
- assertEquals("s5463", species.getElementId());
- assertEquals("Peroxides", species.getName());
- assertEquals(new Integer(0), species.getInitialAmount());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testToXmlSimpleMolecule() throws Exception {
- try {
- String xmlString = readFile(testDirectory + testSimpleMoleculeFile);
- Pair<String, ? extends CellDesignerSpecies<?>> result = parser.parseXmlElement(xmlString);
- CellDesignerSimpleMolecule species = (CellDesignerSimpleMolecule) result.getRight();
-
- String transformedXml = parser.toXml(species.createModelElement("" + idCounter++));
- assertNotNull(transformedXml);
- DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
- DocumentBuilder builder = factory.newDocumentBuilder();
- InputSource is = new InputSource(new StringReader(transformedXml));
- Document doc = builder.parse(is);
- NodeList root = doc.getChildNodes();
- assertEquals("species", root.item(0).getNodeName());
-
- Pair<String, ? extends CellDesignerSpecies<?>> result2 = parser.parseXmlElement(parser.toXml(species.createModelElement("" + idCounter++)));
- CellDesignerSimpleMolecule species2 = (CellDesignerSimpleMolecule) result2.getRight();
-
- assertNotNull(species2);
- assertEquals(species.getName(), species2.getName());
- assertEquals(species.getParent(), species2.getParent());
- assertEquals(species.getInitialAmount(), species2.getInitialAmount());
- assertEquals(species.hasOnlySubstanceUnits(), species2.hasOnlySubstanceUnits());
- assertEquals(species.getCharge(), species2.getCharge());
- assertEquals(species.getInitialConcentration(), species2.getInitialConcentration());
- assertEquals(species.getNotes(), species2.getNotes());
- assertEquals(species.getMiriamData().size(), species2.getMiriamData().size());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testParseXmlSpeciesUnknown() throws Exception {
- try {
- String xmlString = readFile(testDirectory + testUnknownFile);
- Pair<String, ? extends CellDesignerSpecies<?>> result = parser.parseXmlElement(xmlString);
- CellDesignerUnknown species = (CellDesignerUnknown) result.getRight();
- assertEquals("s1356", species.getElementId());
- assertEquals("unidentified caspase acting on Occludin", species.getName());
- assertEquals(new Integer(0), species.getInitialAmount());
- assertEquals(new Integer(0), species.getCharge());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testToXmlUnknown() throws Exception {
- try {
- String xmlString = readFile(testDirectory + testUnknownFile);
- Pair<String, ? extends CellDesignerSpecies<?>> result = parser.parseXmlElement(xmlString);
- CellDesignerUnknown species = (CellDesignerUnknown) result.getRight();
-
- String transformedXml = parser.toXml(species.createModelElement());
- assertNotNull(transformedXml);
- DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
- DocumentBuilder builder = factory.newDocumentBuilder();
- InputSource is = new InputSource(new StringReader(transformedXml));
- Document doc = builder.parse(is);
- NodeList root = doc.getChildNodes();
- assertEquals("species", root.item(0).getNodeName());
-
- Pair<String, ? extends CellDesignerSpecies<?>> result2 = parser.parseXmlElement(parser.toXml(species.createModelElement()));
- CellDesignerUnknown species2 = (CellDesignerUnknown) result2.getRight();
-
- assertNotNull(species2);
- assertEquals(species.getName(), species2.getName());
- assertEquals(species.getParent(), species2.getParent());
- assertEquals(species.getInitialAmount(), species2.getInitialAmount());
- assertEquals(species.hasOnlySubstanceUnits(), species2.hasOnlySubstanceUnits());
- assertEquals(species.getCharge(), species2.getCharge());
- assertEquals(species.getInitialConcentration(), species2.getInitialConcentration());
- assertEquals(species.getNotes(), species2.getNotes());
- assertEquals(species.getMiriamData().size(), species2.getMiriamData().size());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testParseInvalid() throws Exception {
- try {
- String xmlString = readFile("testFiles/invalid/invalid_sbml_protein.xml");
- parser.parseXmlElement(xmlString);
- fail("Exception expected");
- } catch (InvalidXmlSchemaException e) {
- assertTrue(e.getMessage().contains("No annotation node"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testParseInvalid2() throws Exception {
- try {
- String xmlString = readFile("testFiles/invalid/invalid_sbml_protein2.xml");
- parser.parseXmlElement(xmlString);
- fail("Exception expected");
- } catch (InvalidXmlSchemaException e) {
- assertTrue(e.getMessage().contains("bla"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testParseInvalid3() throws Exception {
- try {
- String xmlString = readFile("testFiles/invalid/invalid_sbml_protein3.xml");
- parser.parseXmlElement(xmlString);
- fail("Exception expected");
- } catch (InvalidXmlSchemaException e) {
- assertTrue(e.getMessage().contains("unk_bla"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testParseInvalid4() throws Exception {
- try {
- String xmlString = readFile("testFiles/invalid/invalid_sbml_protein4.xml");
- parser.parseXmlElement(xmlString);
- fail("Exception expected");
- } catch (InvalidXmlSchemaException e) {
- assertTrue(e.getMessage().contains("No celldesigner:extension"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testParseInvalid5() throws Exception {
- try {
- String xmlString = readFile("testFiles/invalid/invalid_sbml_protein5.xml");
- parser.parseXmlElement(xmlString);
- fail("Exception expected");
- } catch (InvalidXmlSchemaException e) {
- assertTrue(e.getMessage().contains("ann_unk"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testParseInvalid6() throws Exception {
- try {
- String xmlString = readFile("testFiles/invalid/invalid_sbml_protein6.xml");
- parser.parseXmlElement(xmlString);
- fail("Exception expected");
- } catch (InvalidXmlSchemaException e) {
- assertTrue(e.getMessage().contains("No celldesigner:speciesIdentity"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testParseInvalid7() throws Exception {
- try {
- String xmlString = readFile("testFiles/invalid/invalid_sbml_protein7.xml");
- parser.parseXmlElement(xmlString);
- fail("Exception expected");
- } catch (InvalidXmlSchemaException e) {
- assertTrue(e.getMessage().contains("unkPos"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testParseInvalid8() throws Exception {
- try {
- String xmlString = readFile("testFiles/invalid/invalid_sbml_protein8.xml");
- parser.parseXmlElement(xmlString);
- fail("Exception expected");
- } catch (InvalidXmlSchemaException e) {
- assertTrue(e.getMessage().contains("Species node in Sbml model doesn't contain"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testParseInvalid9() throws Exception {
- try {
- String xmlString = readFile("testFiles/invalid/invalid_sbml_protein9.xml");
- parser.parseXmlElement(xmlString);
- fail("Exception expected");
- } catch (InvalidXmlSchemaException e) {
- assertTrue(e.getMessage().contains("unknown_protein_class"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testParseInvalid10() throws Exception {
- try {
- String xmlString = readFile("testFiles/invalid/invalid_sbml_protein10.xml");
- parser.parseXmlElement(xmlString);
- fail("Exception expected");
- } catch (InvalidXmlSchemaException e) {
- assertTrue(e.getMessage().contains("Wrong class type for protein reference"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testParseInvalid11() throws Exception {
- try {
- String xmlString = readFile("testFiles/invalid/invalid_sbml_protein11.xml");
- parser.parseXmlElement(xmlString);
- fail("Exception expected");
- } catch (InvalidXmlSchemaException e) {
- assertTrue(e.getMessage().contains("Wrong class type for gene reference"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testParseInvalid12() throws Exception {
- try {
- String xmlString = readFile("testFiles/invalid/invalid_sbml_protein12.xml");
- parser.parseXmlElement(xmlString);
- fail("Exception expected");
- } catch (InvalidXmlSchemaException e) {
- assertTrue(e.getMessage().contains("Wrong class type for rna reference"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testParseInvalid13() throws Exception {
- try {
- String xmlString = readFile("testFiles/invalid/invalid_sbml_protein13.xml");
- parser.parseXmlElement(xmlString);
- fail("Exception expected");
- } catch (InvalidXmlSchemaException e) {
- assertTrue(e.getMessage().contains("Wrong class type for antisense rna reference"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testParseInvalid14() throws Exception {
- try {
- String xmlString = readFile("testFiles/invalid/invalid_sbml_protein14.xml");
- parser.parseXmlElement(xmlString);
- fail("Exception expected");
- } catch (InvalidXmlSchemaException e) {
- assertTrue(e.getMessage().contains("uknNode"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testToXmlWithDefaultCompartment() throws Exception {
- try {
- CellDesignerGenericProtein species = new CellDesignerGenericProtein();
- String xml = parser.toXml(species.createModelElement("EL_ID"));
- assertTrue(xml.contains("EL_ID"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testInvalidSpeciesIdentityToXml() throws Exception {
- try {
- Species species = Mockito.mock(Species.class);
- parser.speciesIdentityToXml(species);
- fail("Excepiton expected");
- } catch (InvalidArgumentException e) {
- assertTrue(e.getMessage().contains("Invalid species class"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testSpeciesIdentityToXml() throws Exception {
- try {
- GenericProtein species = new GenericProtein("xx");
- species.setHypothetical(true);
- String xml = parser.speciesIdentityToXml(species);
- assertTrue(xml.contains("<celldesigner:hypothetical>true</celldesigner:hypothetical>"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testSpeciesStateToXml() throws Exception {
- try {
- SpeciesState state = new SpeciesState();
- state.setHomodimer(2);
- state.setStructuralState("xxxState");
- String xml = parser.speciesStateToXml(state);
- assertTrue(xml.contains("xxxState"));
- assertTrue(xml.contains("celldesigner:homodimer"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testProcessInvalidStateDataInSpecies() throws Exception {
- try {
- SpeciesState state = new SpeciesState();
- state.addModificationResidue(new CellDesignerModificationResidue());
- CellDesignerComplexSpecies species = new CellDesignerComplexSpecies();
-
- parser.processStateDataInSpecies(species, state);
- fail("Exception expected");
- } catch (NotImplementedException e) {
- assertTrue(e.getMessage().contains("Modification not supported in Complex"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testProcessInvalidStateDataInSpecies2() throws Exception {
- try {
- SpeciesState state = new SpeciesState();
- state.setStructuralState("state");
- CellDesignerGene species = new CellDesignerGene();
-
- parser.processStateDataInSpecies(species, state);
- fail("Exception expected");
- } catch (NotImplementedException e) {
- assertTrue(e.getMessage().contains("StructuralState not supported in Gene"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testProcessInvalidStateDataInSpecies3() throws Exception {
- try {
- SpeciesState state = new SpeciesState();
- state.setStructuralState("state");
- CellDesignerRna species = new CellDesignerRna();
-
- parser.processStateDataInSpecies(species, state);
- fail("Exception expected");
- } catch (NotImplementedException e) {
- assertTrue(e.getMessage().contains("Structural state not supported in RNA"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testProcessInvalidStateDataInSpecies4() throws Exception {
- try {
- SpeciesState state = new SpeciesState();
- state.addModificationResidue(new CellDesignerModificationResidue());
- CellDesignerSimpleMolecule species = new CellDesignerSimpleMolecule();
-
- parser.processStateDataInSpecies(species, state);
- fail("Exception expected");
- } catch (NotImplementedException e) {
- assertTrue(e.getMessage().contains("Modification not supported in SimpleMolecule"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testProcessInvalidStateDataInSpecies5() throws Exception {
- try {
- SpeciesState state = new SpeciesState();
- state.setStructuralState("state");
- CellDesignerSimpleMolecule species = new CellDesignerSimpleMolecule();
-
- parser.processStateDataInSpecies(species, state);
- fail("Exception expected");
- } catch (NotImplementedException e) {
- assertTrue(e.getMessage().contains("Structural state not supported in SimpleMolecule"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testProcessInvalidStateDataInSpecies6() throws Exception {
- try {
- SpeciesState state = new SpeciesState();
- state.setStructuralState("state");
- CellDesignerAntisenseRna species = new CellDesignerAntisenseRna();
-
- parser.processStateDataInSpecies(species, state);
- fail("Exception expected");
- } catch (NotImplementedException e) {
- assertTrue(e.getMessage().contains("Structural state not supported in AntisenseRna"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testProcessInvalidStateDataInSpecies7() throws Exception {
- try {
- SpeciesState state = new SpeciesState();
- state.setStructuralState("state");
- CellDesignerSpecies<?> species = new CellDesignerSpecies<Gene>();
-
- parser.processStateDataInSpecies(species, state);
- fail("Exception expected");
- } catch (NotImplementedException e) {
- assertTrue(e.getMessage().contains("Structural state not supported"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testProcessInvalidStateDataInSpecies8() throws Exception {
- try {
- SpeciesState state = new SpeciesState();
- state.addModificationResidue(new CellDesignerModificationResidue());
- CellDesignerSpecies<?> species = new CellDesignerSpecies<Gene>();
-
- parser.processStateDataInSpecies(species, state);
- fail("Exception expected");
- } catch (NotImplementedException e) {
- assertTrue(e.getMessage().contains("Modification not supported in"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testProcessAntisenseRnaStateDataInSpecies() throws Exception {
- try {
- SpeciesState state = new SpeciesState();
- state.addModificationResidue(new CellDesignerModificationResidue());
- CellDesignerAntisenseRna species = new CellDesignerAntisenseRna();
-
- parser.processStateDataInSpecies(species, state);
-
- assertEquals(1, species.getRegions().size());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCreateRnaRegion() throws Exception {
- try {
- CellDesignerModificationResidue mr = new CellDesignerModificationResidue();
- mr.setSize(1.0);
- mr.setAngle(1.0);
-
- CellDesignerRnaRegion region = parser.createRnaRegion(mr);
- assertNotNull(region.getPos());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCreateAntisenseRnaRegion() throws Exception {
- try {
- CellDesignerModificationResidue mr = new CellDesignerModificationResidue();
- mr.setSize(1.0);
- mr.setAngle(1.0);
-
- CellDesignerAntisenseRnaRegion region = parser.createAntisenseRnaRegion(mr);
- assertNotNull(region.getPos());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
+ @SuppressWarnings("unused")
+ private Logger logger = Logger.getLogger(SpeciesSbmlParserTest.class.getName());
+
+ SpeciesSbmlParser parser;
+
+ String testDirectory = "testFiles" + System.getProperty("file.separator") + "xmlNodeTestExamples"
+ + System.getProperty("file.separator");
+ String testGeneFile = "sbml_gene.xml";
+ String testDegradedFile = "sbml_degraded.xml";
+ String testDrugFile = "sbml_drug.xml";
+ String testIonFile = "sbml_ion.xml";
+ String testPhenotypeFile = "sbml_phenotype.xml";
+ String testProteinFile = "sbml_protein.xml";
+ String testRnaFile = "sbml_rna.xml";
+ String testSimpleMoleculeFile = "sbml_simple_molecule.xml";
+ String testUnknownFile = "sbml_unknown.xml";
+
+ CellDesignerElementCollection elements;
+
+ int idCounter = 0;
+
+ @Before
+ public void setUp() throws Exception {
+ elements = new CellDesignerElementCollection();
+ parser = new SpeciesSbmlParser(elements);
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testParseXmlSpeciesAntisenseRna() throws Exception {
+ try {
+ String xmlString = readFile(testDirectory + "sbml_antisense_rna.xml");
+ Pair<String, ? extends CellDesignerSpecies<?>> result = parser.parseXmlElement(xmlString);
+ CellDesignerAntisenseRna species = (CellDesignerAntisenseRna) result.getRight();
+ assertEquals("s2", species.getElementId());
+ assertEquals("s3", species.getName());
+ assertEquals(2, species.getInitialAmount(), Configuration.EPSILON);
+ assertEquals(Boolean.TRUE, species.hasOnlySubstanceUnits());
+ assertEquals(new Integer(0), species.getCharge());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testParseXmlSpeciesWithKineticsData() throws Exception {
+ try {
+ String xmlString = readFile("testFiles/kinetics/species_with_kinetics_param.xml");
+ Pair<String, ? extends CellDesignerSpecies<?>> result = parser.parseXmlElement(xmlString);
+ CellDesignerProtein<?> species = (CellDesignerProtein<?>) result.getRight();
+ assertEquals(3.7, species.getInitialConcentration(), Configuration.EPSILON);
+ assertEquals(SbmlUnitType.MOLE, species.getSubstanceUnit());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testParseXmlSpeciesWithKineticsData2() throws Exception {
+ try {
+ String xmlString = readFile("testFiles/kinetics/species_with_kinetics_param2.xml");
+ Pair<String, ? extends CellDesignerSpecies<?>> result = parser.parseXmlElement(xmlString);
+ CellDesignerProtein<?> species = (CellDesignerProtein<?>) result.getRight();
+ assertEquals(2.5, species.getInitialAmount(), Configuration.EPSILON);
+ assertEquals(SbmlUnitType.GRAM, species.getSubstanceUnit());
+ assertEquals(Boolean.TRUE, species.hasOnlySubstanceUnits());
+ assertEquals("Boundary condition wasn't parsed", Boolean.TRUE, species.isBoundaryCondition());
+ assertEquals("Constant property wasn't parsed", Boolean.TRUE, species.isConstant());
+ assertEquals(new Integer(0), species.getCharge());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testToXmlAntisenseRna() throws Exception {
+ try {
+ String xmlString = readFile(testDirectory + "sbml_antisense_rna.xml");
+ Pair<String, ? extends CellDesignerSpecies<?>> result = parser.parseXmlElement(xmlString);
+ CellDesignerAntisenseRna species = (CellDesignerAntisenseRna) result.getRight();
+
+ String transformedXml = parser.toXml(species.createModelElement());
+ assertNotNull(transformedXml);
+ DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
+ DocumentBuilder builder = factory.newDocumentBuilder();
+ InputSource is = new InputSource(new StringReader(transformedXml));
+ Document doc = builder.parse(is);
+ NodeList root = doc.getChildNodes();
+ assertEquals("species", root.item(0).getNodeName());
+
+ Pair<String, ? extends CellDesignerSpecies<?>> result2 = parser
+ .parseXmlElement(parser.toXml(species.createModelElement()));
+ CellDesignerAntisenseRna species2 = (CellDesignerAntisenseRna) result2.getRight();
+
+ assertEquals(species.getName(), species2.getName());
+ assertEquals(species.getParent(), species2.getParent());
+ assertEquals(species.getInitialAmount(), species2.getInitialAmount());
+ assertEquals(species.hasOnlySubstanceUnits(), species2.hasOnlySubstanceUnits());
+ assertEquals(species.getCharge(), species2.getCharge());
+ assertEquals(species.getPositionToCompartment(), species2.getPositionToCompartment());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testParseXmlSpeciesComplex() throws Exception {
+ try {
+ String xmlString = readFile(testDirectory + "sbml_complex.xml");
+ Pair<String, ? extends CellDesignerSpecies<?>> result = parser.parseXmlElement(xmlString);
+ CellDesignerComplexSpecies species = (CellDesignerComplexSpecies) result.getRight();
+ assertNotNull(species);
+ assertEquals("s6549", species.getElementId());
+ assertEquals("LC3-II", species.getName());
+ assertEquals(0.0, species.getInitialAmount(), Configuration.EPSILON);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testToXmlComplex() throws Exception {
+ try {
+ String xmlString = readFile(testDirectory + "sbml_complex.xml");
+ Pair<String, ? extends CellDesignerSpecies<?>> result = parser.parseXmlElement(xmlString);
+ CellDesignerComplexSpecies species = (CellDesignerComplexSpecies) result.getRight();
+
+ String transformedXml = parser.toXml(species.createModelElement());
+ assertNotNull(transformedXml);
+ DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
+ DocumentBuilder builder = factory.newDocumentBuilder();
+ InputSource is = new InputSource(new StringReader(transformedXml));
+ Document doc = builder.parse(is);
+ NodeList root = doc.getChildNodes();
+ assertEquals("species", root.item(0).getNodeName());
+
+ Pair<String, ? extends CellDesignerSpecies<?>> result2 = parser
+ .parseXmlElement(parser.toXml(species.createModelElement()));
+ CellDesignerComplexSpecies species2 = (CellDesignerComplexSpecies) result2.getRight();
+
+ assertNotNull(species2);
+ assertEquals(species.getName(), species2.getName());
+ assertEquals(species.getParent(), species2.getParent());
+ assertEquals(species.getInitialAmount(), species2.getInitialAmount());
+ assertEquals(species.hasOnlySubstanceUnits(), species2.hasOnlySubstanceUnits());
+ assertEquals(species.getCharge(), species2.getCharge());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testParseXmlSpeciesDegraded() throws Exception {
+ try {
+ String xmlString = readFile(testDirectory + testDegradedFile);
+ Pair<String, ? extends CellDesignerSpecies<?>> result = parser.parseXmlElement(xmlString);
+ CellDesignerDegraded species = (CellDesignerDegraded) result.getRight();
+ assertNotNull(species);
+ assertEquals("s1275", species.getElementId());
+ assertEquals("s1275", species.getName());
+ assertEquals(0, species.getInitialAmount(), Configuration.EPSILON);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testToXmlDegraded() throws Exception {
+ try {
+ String xmlString = readFile(testDirectory + testDegradedFile);
+ Pair<String, ? extends CellDesignerSpecies<?>> result = parser.parseXmlElement(xmlString);
+ CellDesignerDegraded species = (CellDesignerDegraded) result.getRight();
+
+ String transformedXml = parser.toXml(species.createModelElement());
+ assertNotNull(transformedXml);
+ DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
+ DocumentBuilder builder = factory.newDocumentBuilder();
+ InputSource is = new InputSource(new StringReader(transformedXml));
+ Document doc = builder.parse(is);
+ NodeList root = doc.getChildNodes();
+ assertEquals("species", root.item(0).getNodeName());
+
+ Pair<String, ? extends CellDesignerSpecies<?>> result2 = parser
+ .parseXmlElement(parser.toXml(species.createModelElement()));
+ CellDesignerDegraded species2 = (CellDesignerDegraded) result2.getRight();
+
+ assertNotNull(species2);
+ assertEquals(species.getName(), species2.getName());
+ assertEquals(species.getParent(), species2.getParent());
+ assertEquals(species.getInitialAmount(), species2.getInitialAmount());
+ assertEquals(species.hasOnlySubstanceUnits(), species2.hasOnlySubstanceUnits());
+ assertEquals(species.getCharge(), species2.getCharge());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testParseXmlSpeciesDrug() throws Exception {
+ try {
+ String xmlString = readFile(testDirectory + testDrugFile);
+ Pair<String, ? extends CellDesignerSpecies<?>> result = parser.parseXmlElement(xmlString);
+ CellDesignerDrug species = (CellDesignerDrug) result.getRight();
+ assertEquals("s6104", species.getElementId());
+ assertEquals("geldanamycin", species.getName());
+ assertEquals(new Integer(0), species.getCharge());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testToXmlDrug() throws Exception {
+ try {
+ String xmlString = readFile(testDirectory + testDrugFile);
+ Pair<String, ? extends CellDesignerSpecies<?>> result = parser.parseXmlElement(xmlString);
+ CellDesignerDrug species = (CellDesignerDrug) result.getRight();
+
+ String transformedXml = parser.toXml(species.createModelElement());
+ assertNotNull(transformedXml);
+ DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
+ DocumentBuilder builder = factory.newDocumentBuilder();
+ InputSource is = new InputSource(new StringReader(transformedXml));
+ Document doc = builder.parse(is);
+ NodeList root = doc.getChildNodes();
+ assertEquals("species", root.item(0).getNodeName());
+
+ Pair<String, ? extends CellDesignerSpecies<?>> result2 = parser
+ .parseXmlElement(parser.toXml(species.createModelElement()));
+ CellDesignerDrug species2 = (CellDesignerDrug) result2.getRight();
+
+ assertNotNull(species2);
+ assertEquals(species.getName(), species2.getName());
+ assertEquals(species.getParent(), species2.getParent());
+ assertEquals(species.getInitialAmount(), species2.getInitialAmount());
+ assertEquals(species.hasOnlySubstanceUnits(), species2.hasOnlySubstanceUnits());
+ assertEquals(species.getCharge(), species2.getCharge());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testParseXmlSpeciesGene() throws Exception {
+ try {
+ String xmlString = readFile(testDirectory + testGeneFile);
+ Pair<String, ? extends CellDesignerSpecies<?>> result = parser.parseXmlElement(xmlString);
+ CellDesignerGene species = (CellDesignerGene) result.getRight();
+
+ assertEquals("s5916", species.getElementId());
+ assertEquals("Ptgr1", species.getName());
+ assertEquals(new Integer(0), species.getCharge());
+ assertEquals(0, species.getInitialAmount(), Configuration.EPSILON);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testParseXmlSpeciesGeneWithModelUpdate() throws Exception {
+ try {
+ CellDesignerSpecies<?> gene = new CellDesignerGene();
+ gene.setElementId("s5916");
+ InternalModelSpeciesData modelData = new InternalModelSpeciesData();
+ modelData.updateSpecies(gene, "");
+
+ SpeciesSbmlParser complexParser = new SpeciesSbmlParser(elements);
+ CellDesignerGene oldGene = new CellDesignerGene();
+ oldGene.setElementId("s5916");
+ oldGene.setName("Ptgr1");
+ modelData.updateSpecies(oldGene, "gn95");
+
+ String xmlString = readFile(testDirectory + testGeneFile);
+ Pair<String, ? extends CellDesignerSpecies<?>> result = complexParser.parseXmlElement(xmlString);
+ CellDesignerGene species = (CellDesignerGene) result.getRight();
+ modelData.updateSpecies(species, result.getLeft());
+
+ assertEquals("s5916", species.getElementId());
+ assertEquals("Ptgr1", species.getName());
+ assertTrue(species.getNotes().contains("prostaglandin reductase 1"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testToXmlGene() throws Exception {
+ try {
+ String xmlString = readFile(testDirectory + testGeneFile);
+ Pair<String, ? extends CellDesignerSpecies<?>> result = parser.parseXmlElement(xmlString);
+ CellDesignerGene species = (CellDesignerGene) result.getRight();
+
+ String transformedXml = parser.toXml(species.createModelElement());
+ assertNotNull(transformedXml);
+ DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
+ DocumentBuilder builder = factory.newDocumentBuilder();
+ InputSource is = new InputSource(new StringReader(transformedXml));
+ Document doc = builder.parse(is);
+ NodeList root = doc.getChildNodes();
+ assertEquals("species", root.item(0).getNodeName());
+
+ Pair<String, ? extends CellDesignerSpecies<?>> result2 = parser
+ .parseXmlElement(parser.toXml(species.createModelElement()));
+ CellDesignerGene species2 = (CellDesignerGene) result2.getRight();
+
+ assertNotNull(species2);
+ assertEquals(species.getName(), species2.getName());
+ assertEquals(species.getParent(), species2.getParent());
+ assertEquals(species.getInitialAmount(), species2.getInitialAmount());
+ assertEquals(species.hasOnlySubstanceUnits(), species2.hasOnlySubstanceUnits());
+ assertEquals(species.getCharge(), species2.getCharge());
+ assertTrue(species2.getNotes().trim().contains(species.getNotes().trim()));
+ assertEquals(species.getMiriamData().size(), species2.getMiriamData().size());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testParseXmlSpeciesIon() throws Exception {
+ try {
+ String xmlString = readFile(testDirectory + testIonFile);
+ Pair<String, ? extends CellDesignerSpecies<?>> result = parser.parseXmlElement(xmlString);
+ CellDesignerIon species = (CellDesignerIon) result.getRight();
+
+ assertEquals("s6029", species.getElementId());
+ assertEquals("Pi", species.getName());
+ assertEquals(new Integer(0), species.getCharge());
+ assertEquals(0, species.getInitialConcentration(), Configuration.EPSILON);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testToXmlIon() throws Exception {
+ try {
+ String xmlString = readFile(testDirectory + testIonFile);
+ Pair<String, ? extends CellDesignerSpecies<?>> result = parser.parseXmlElement(xmlString);
+ CellDesignerIon species = (CellDesignerIon) result.getRight();
+
+ String transformedXml = parser.toXml(species.createModelElement());
+ assertNotNull(transformedXml);
+ DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
+ DocumentBuilder builder = factory.newDocumentBuilder();
+ InputSource is = new InputSource(new StringReader(transformedXml));
+ Document doc = builder.parse(is);
+ NodeList root = doc.getChildNodes();
+ assertEquals("species", root.item(0).getNodeName());
+
+ Pair<String, ? extends CellDesignerSpecies<?>> result2 = parser.parseXmlElement(xmlString);
+ CellDesignerIon species2 = (CellDesignerIon) result2.getRight();
+
+ assertNotNull(species2);
+ assertEquals(species.getElementId(), species2.getElementId());
+ assertEquals(species.getName(), species2.getName());
+ assertEquals(species.getParent(), species2.getParent());
+ assertEquals(species.getInitialAmount(), species2.getInitialAmount());
+ assertEquals(species.hasOnlySubstanceUnits(), species2.hasOnlySubstanceUnits());
+ assertEquals(species.getCharge(), species2.getCharge());
+ assertEquals(species.getInitialConcentration(), species2.getInitialConcentration());
+ assertEquals(species.getNotes().trim(), species2.getNotes().trim());
+ assertEquals(species.getMiriamData().size(), species2.getMiriamData().size());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testParseXmlSpeciesPhenotype() throws Exception {
+ try {
+ String xmlString = readFile(testDirectory + testPhenotypeFile);
+ Pair<String, ? extends CellDesignerSpecies<?>> result = parser.parseXmlElement(xmlString);
+ CellDesignerPhenotype species = (CellDesignerPhenotype) result.getRight();
+
+ assertEquals("s5462", species.getElementId());
+ assertEquals("Neuronal damage and death", species.getName());
+ assertEquals(0, species.getInitialAmount(), Configuration.EPSILON);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testToXmlPhenotype() throws Exception {
+ try {
+ String xmlString = readFile(testDirectory + testPhenotypeFile);
+ Pair<String, ? extends CellDesignerSpecies<?>> result = parser.parseXmlElement(xmlString);
+ CellDesignerPhenotype species = (CellDesignerPhenotype) result.getRight();
+
+ String transformedXml = parser.toXml(species.createModelElement());
+ assertNotNull(transformedXml);
+ DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
+ DocumentBuilder builder = factory.newDocumentBuilder();
+ InputSource is = new InputSource(new StringReader(transformedXml));
+ Document doc = builder.parse(is);
+ NodeList root = doc.getChildNodes();
+ assertEquals("species", root.item(0).getNodeName());
+
+ Pair<String, ? extends CellDesignerSpecies<?>> result2 = parser
+ .parseXmlElement(parser.toXml(species.createModelElement()));
+ CellDesignerPhenotype species2 = (CellDesignerPhenotype) result2.getRight();
+
+ assertNotNull(species2);
+ assertEquals(species.getName(), species2.getName());
+ assertEquals(species.getParent(), species2.getParent());
+ assertEquals(species.getInitialAmount(), species2.getInitialAmount());
+ assertEquals(species.hasOnlySubstanceUnits(), species2.hasOnlySubstanceUnits());
+ assertEquals(species.getCharge(), species2.getCharge());
+ assertEquals(species.getInitialConcentration(), species2.getInitialConcentration());
+ assertEquals(species.getNotes(), species2.getNotes());
+ assertEquals(species.getMiriamData().size(), species2.getMiriamData().size());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testParseXmlSpeciesProtein() throws Exception {
+ try {
+ String xmlString = readFile(testDirectory + testProteinFile);
+ Pair<String, ? extends CellDesignerSpecies<?>> result = parser.parseXmlElement(xmlString);
+ CellDesignerProtein<?> species = (CellDesignerProtein<?>) result.getRight();
+
+ assertEquals("s5456", species.getElementId());
+ assertEquals("PTPRC", species.getName());
+ assertEquals(0, species.getInitialAmount(), Configuration.EPSILON);
+ assertEquals(new Integer(0), species.getCharge());
+ assertTrue(species.getNotes().contains("protein tyrosine phosphatase, receptor type, C"));
+ assertNull(species.getStructuralState());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testToXmlProtein() throws Exception {
+ try {
+ String xmlString = readFile(testDirectory + testProteinFile);
+ Pair<String, ? extends CellDesignerSpecies<?>> result = parser.parseXmlElement(xmlString);
+ CellDesignerGenericProtein species = new CellDesignerGenericProtein(result.getRight());
+
+ String transformedXml = parser.toXml(species.createModelElement("" + idCounter++));
+ assertNotNull(transformedXml);
+ DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
+ DocumentBuilder builder = factory.newDocumentBuilder();
+ InputSource is = new InputSource(new StringReader(transformedXml));
+ Document doc = builder.parse(is);
+ NodeList root = doc.getChildNodes();
+ assertEquals("species", root.item(0).getNodeName());
+
+ Pair<String, ? extends CellDesignerSpecies<?>> result2 = parser
+ .parseXmlElement(parser.toXml(species.createModelElement("" + idCounter++)));
+ CellDesignerProtein<?> species2 = (CellDesignerProtein<?>) result2.getRight();
+
+ assertNotNull(species2);
+ assertEquals(species.getName(), species2.getName());
+ assertEquals(species.getParent(), species2.getParent());
+ assertEquals(species.getInitialAmount(), species2.getInitialAmount());
+ assertEquals(species.hasOnlySubstanceUnits(), species2.hasOnlySubstanceUnits());
+ assertEquals(species.getCharge(), species2.getCharge());
+ assertEquals(species.getInitialConcentration(), species2.getInitialConcentration());
+ assertTrue(species2.getNotes().contains(species.getNotes()));
+ assertEquals(species.getMiriamData().size(), species2.getMiriamData().size());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testParseXmlSpeciesRna() throws Exception {
+ try {
+ String xmlString = readFile(testDirectory + testRnaFile);
+ Pair<String, ? extends CellDesignerSpecies<?>> result = parser.parseXmlElement(xmlString);
+ CellDesignerRna species = (CellDesignerRna) result.getRight();
+
+ assertEquals("s5914", species.getElementId());
+ assertEquals("Fmo3", species.getName());
+ assertEquals(0, species.getInitialAmount(), Configuration.EPSILON);
+ assertEquals(new Integer(0), species.getCharge());
+ assertTrue(species.getNotes().contains("Dimethylaniline monooxygenase [N-oxide-forming] 3"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testToXmlRna() throws Exception {
+ try {
+ String xmlString = readFile(testDirectory + testRnaFile);
+ Pair<String, ? extends CellDesignerSpecies<?>> result = parser.parseXmlElement(xmlString);
+ CellDesignerRna species = (CellDesignerRna) result.getRight();
+
+ String transformedXml = parser.toXml(species.createModelElement());
+ assertNotNull(transformedXml);
+ DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
+ DocumentBuilder builder = factory.newDocumentBuilder();
+ InputSource is = new InputSource(new StringReader(transformedXml));
+ Document doc = builder.parse(is);
+ NodeList root = doc.getChildNodes();
+ assertEquals("species", root.item(0).getNodeName());
+
+ Pair<String, ? extends CellDesignerSpecies<?>> result2 = parser
+ .parseXmlElement(parser.toXml(species.createModelElement()));
+ CellDesignerRna species2 = (CellDesignerRna) result2.getRight();
+
+ assertNotNull(species2);
+ assertEquals(species.getName(), species2.getName());
+ assertEquals(species.getParent(), species2.getParent());
+ assertEquals(species.getInitialAmount(), species2.getInitialAmount());
+ assertEquals(species.hasOnlySubstanceUnits(), species2.hasOnlySubstanceUnits());
+ assertEquals(species.getCharge(), species2.getCharge());
+ assertEquals(species.getInitialConcentration(), species2.getInitialConcentration());
+ assertTrue(species2.getNotes().trim().contains(species.getNotes().trim()));
+ assertEquals(species.getMiriamData().size(), species2.getMiriamData().size());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testParseXmlSpeciesSimpleMolecule() throws Exception {
+ try {
+ String xmlString = readFile(testDirectory + testSimpleMoleculeFile);
+ Pair<String, ? extends CellDesignerSpecies<?>> result = parser.parseXmlElement(xmlString);
+ CellDesignerSimpleMolecule species = (CellDesignerSimpleMolecule) result.getRight();
+ assertEquals("s5463", species.getElementId());
+ assertEquals("Peroxides", species.getName());
+ assertEquals(0, species.getInitialAmount(), Configuration.EPSILON);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testToXmlSimpleMolecule() throws Exception {
+ try {
+ String xmlString = readFile(testDirectory + testSimpleMoleculeFile);
+ Pair<String, ? extends CellDesignerSpecies<?>> result = parser.parseXmlElement(xmlString);
+ CellDesignerSimpleMolecule species = (CellDesignerSimpleMolecule) result.getRight();
+
+ String transformedXml = parser.toXml(species.createModelElement("" + idCounter++));
+ assertNotNull(transformedXml);
+ DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
+ DocumentBuilder builder = factory.newDocumentBuilder();
+ InputSource is = new InputSource(new StringReader(transformedXml));
+ Document doc = builder.parse(is);
+ NodeList root = doc.getChildNodes();
+ assertEquals("species", root.item(0).getNodeName());
+
+ Pair<String, ? extends CellDesignerSpecies<?>> result2 = parser
+ .parseXmlElement(parser.toXml(species.createModelElement("" + idCounter++)));
+ CellDesignerSimpleMolecule species2 = (CellDesignerSimpleMolecule) result2.getRight();
+
+ assertNotNull(species2);
+ assertEquals(species.getName(), species2.getName());
+ assertEquals(species.getParent(), species2.getParent());
+ assertEquals(species.getInitialAmount(), species2.getInitialAmount());
+ assertEquals(species.hasOnlySubstanceUnits(), species2.hasOnlySubstanceUnits());
+ assertEquals(species.getCharge(), species2.getCharge());
+ assertEquals(species.getInitialConcentration(), species2.getInitialConcentration());
+ assertEquals(species.getNotes(), species2.getNotes());
+ assertEquals(species.getMiriamData().size(), species2.getMiriamData().size());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testParseXmlSpeciesUnknown() throws Exception {
+ try {
+ String xmlString = readFile(testDirectory + testUnknownFile);
+ Pair<String, ? extends CellDesignerSpecies<?>> result = parser.parseXmlElement(xmlString);
+ CellDesignerUnknown species = (CellDesignerUnknown) result.getRight();
+ assertEquals("s1356", species.getElementId());
+ assertEquals("unidentified caspase acting on Occludin", species.getName());
+ assertEquals(0, species.getInitialAmount(), Configuration.EPSILON);
+ assertEquals(new Integer(0), species.getCharge());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testToXmlUnknown() throws Exception {
+ try {
+ String xmlString = readFile(testDirectory + testUnknownFile);
+ Pair<String, ? extends CellDesignerSpecies<?>> result = parser.parseXmlElement(xmlString);
+ CellDesignerUnknown species = (CellDesignerUnknown) result.getRight();
+
+ String transformedXml = parser.toXml(species.createModelElement());
+ assertNotNull(transformedXml);
+ DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
+ DocumentBuilder builder = factory.newDocumentBuilder();
+ InputSource is = new InputSource(new StringReader(transformedXml));
+ Document doc = builder.parse(is);
+ NodeList root = doc.getChildNodes();
+ assertEquals("species", root.item(0).getNodeName());
+
+ Pair<String, ? extends CellDesignerSpecies<?>> result2 = parser
+ .parseXmlElement(parser.toXml(species.createModelElement()));
+ CellDesignerUnknown species2 = (CellDesignerUnknown) result2.getRight();
+
+ assertNotNull(species2);
+ assertEquals(species.getName(), species2.getName());
+ assertEquals(species.getParent(), species2.getParent());
+ assertEquals(species.getInitialAmount(), species2.getInitialAmount());
+ assertEquals(species.hasOnlySubstanceUnits(), species2.hasOnlySubstanceUnits());
+ assertEquals(species.getCharge(), species2.getCharge());
+ assertEquals(species.getInitialConcentration(), species2.getInitialConcentration());
+ assertEquals(species.getNotes(), species2.getNotes());
+ assertEquals(species.getMiriamData().size(), species2.getMiriamData().size());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testParseInvalid() throws Exception {
+ try {
+ String xmlString = readFile("testFiles/invalid/invalid_sbml_protein.xml");
+ parser.parseXmlElement(xmlString);
+ fail("Exception expected");
+ } catch (InvalidXmlSchemaException e) {
+ assertTrue(e.getMessage().contains("No annotation node"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testParseInvalid2() throws Exception {
+ try {
+ String xmlString = readFile("testFiles/invalid/invalid_sbml_protein2.xml");
+ parser.parseXmlElement(xmlString);
+ fail("Exception expected");
+ } catch (InvalidXmlSchemaException e) {
+ assertTrue(e.getMessage().contains("bla"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testParseInvalid3() throws Exception {
+ try {
+ String xmlString = readFile("testFiles/invalid/invalid_sbml_protein3.xml");
+ parser.parseXmlElement(xmlString);
+ fail("Exception expected");
+ } catch (InvalidXmlSchemaException e) {
+ assertTrue(e.getMessage().contains("unk_bla"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testParseInvalid4() throws Exception {
+ try {
+ String xmlString = readFile("testFiles/invalid/invalid_sbml_protein4.xml");
+ parser.parseXmlElement(xmlString);
+ fail("Exception expected");
+ } catch (InvalidXmlSchemaException e) {
+ assertTrue(e.getMessage().contains("No celldesigner:extension"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testParseInvalid5() throws Exception {
+ try {
+ String xmlString = readFile("testFiles/invalid/invalid_sbml_protein5.xml");
+ parser.parseXmlElement(xmlString);
+ fail("Exception expected");
+ } catch (InvalidXmlSchemaException e) {
+ assertTrue(e.getMessage().contains("ann_unk"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testParseInvalid6() throws Exception {
+ try {
+ String xmlString = readFile("testFiles/invalid/invalid_sbml_protein6.xml");
+ parser.parseXmlElement(xmlString);
+ fail("Exception expected");
+ } catch (InvalidXmlSchemaException e) {
+ assertTrue(e.getMessage().contains("No celldesigner:speciesIdentity"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testParseInvalid7() throws Exception {
+ try {
+ String xmlString = readFile("testFiles/invalid/invalid_sbml_protein7.xml");
+ parser.parseXmlElement(xmlString);
+ fail("Exception expected");
+ } catch (InvalidXmlSchemaException e) {
+ assertTrue(e.getMessage().contains("unkPos"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testParseInvalid8() throws Exception {
+ try {
+ String xmlString = readFile("testFiles/invalid/invalid_sbml_protein8.xml");
+ parser.parseXmlElement(xmlString);
+ fail("Exception expected");
+ } catch (InvalidXmlSchemaException e) {
+ assertTrue(e.getMessage().contains("Species node in Sbml model doesn't contain"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testParseInvalid9() throws Exception {
+ try {
+ String xmlString = readFile("testFiles/invalid/invalid_sbml_protein9.xml");
+ parser.parseXmlElement(xmlString);
+ fail("Exception expected");
+ } catch (InvalidXmlSchemaException e) {
+ assertTrue(e.getMessage().contains("unknown_protein_class"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testParseInvalid10() throws Exception {
+ try {
+ String xmlString = readFile("testFiles/invalid/invalid_sbml_protein10.xml");
+ parser.parseXmlElement(xmlString);
+ fail("Exception expected");
+ } catch (InvalidXmlSchemaException e) {
+ assertTrue(e.getMessage().contains("Wrong class type for protein reference"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testParseInvalid11() throws Exception {
+ try {
+ String xmlString = readFile("testFiles/invalid/invalid_sbml_protein11.xml");
+ parser.parseXmlElement(xmlString);
+ fail("Exception expected");
+ } catch (InvalidXmlSchemaException e) {
+ assertTrue(e.getMessage().contains("Wrong class type for gene reference"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testParseInvalid12() throws Exception {
+ try {
+ String xmlString = readFile("testFiles/invalid/invalid_sbml_protein12.xml");
+ parser.parseXmlElement(xmlString);
+ fail("Exception expected");
+ } catch (InvalidXmlSchemaException e) {
+ assertTrue(e.getMessage().contains("Wrong class type for rna reference"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testParseInvalid13() throws Exception {
+ try {
+ String xmlString = readFile("testFiles/invalid/invalid_sbml_protein13.xml");
+ parser.parseXmlElement(xmlString);
+ fail("Exception expected");
+ } catch (InvalidXmlSchemaException e) {
+ assertTrue(e.getMessage().contains("Wrong class type for antisense rna reference"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testParseInvalid14() throws Exception {
+ try {
+ String xmlString = readFile("testFiles/invalid/invalid_sbml_protein14.xml");
+ parser.parseXmlElement(xmlString);
+ fail("Exception expected");
+ } catch (InvalidXmlSchemaException e) {
+ assertTrue(e.getMessage().contains("uknNode"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testToXmlWithDefaultCompartment() throws Exception {
+ try {
+ CellDesignerGenericProtein species = new CellDesignerGenericProtein();
+ String xml = parser.toXml(species.createModelElement("EL_ID"));
+ assertTrue(xml.contains("EL_ID"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testInvalidSpeciesIdentityToXml() throws Exception {
+ try {
+ Species species = Mockito.mock(Species.class);
+ parser.speciesIdentityToXml(species);
+ fail("Excepiton expected");
+ } catch (InvalidArgumentException e) {
+ assertTrue(e.getMessage().contains("Invalid species class"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testSpeciesIdentityToXml() throws Exception {
+ try {
+ GenericProtein species = new GenericProtein("xx");
+ species.setHypothetical(true);
+ String xml = parser.speciesIdentityToXml(species);
+ assertTrue(xml.contains("<celldesigner:hypothetical>true</celldesigner:hypothetical>"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testSpeciesStateToXml() throws Exception {
+ try {
+ SpeciesState state = new SpeciesState();
+ state.setHomodimer(2);
+ state.setStructuralState("xxxState");
+ String xml = parser.speciesStateToXml(state);
+ assertTrue(xml.contains("xxxState"));
+ assertTrue(xml.contains("celldesigner:homodimer"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testProcessInvalidStateDataInSpecies() throws Exception {
+ try {
+ SpeciesState state = new SpeciesState();
+ state.addModificationResidue(new CellDesignerModificationResidue());
+ CellDesignerComplexSpecies species = new CellDesignerComplexSpecies();
+
+ parser.processStateDataInSpecies(species, state);
+ fail("Exception expected");
+ } catch (NotImplementedException e) {
+ assertTrue(e.getMessage().contains("Modification not supported in Complex"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testProcessInvalidStateDataInSpecies2() throws Exception {
+ try {
+ SpeciesState state = new SpeciesState();
+ state.setStructuralState("state");
+ CellDesignerGene species = new CellDesignerGene();
+
+ parser.processStateDataInSpecies(species, state);
+ fail("Exception expected");
+ } catch (NotImplementedException e) {
+ assertTrue(e.getMessage().contains("StructuralState not supported in Gene"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testProcessInvalidStateDataInSpecies3() throws Exception {
+ try {
+ SpeciesState state = new SpeciesState();
+ state.setStructuralState("state");
+ CellDesignerRna species = new CellDesignerRna();
+
+ parser.processStateDataInSpecies(species, state);
+ fail("Exception expected");
+ } catch (NotImplementedException e) {
+ assertTrue(e.getMessage().contains("Structural state not supported in RNA"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testProcessInvalidStateDataInSpecies4() throws Exception {
+ try {
+ SpeciesState state = new SpeciesState();
+ state.addModificationResidue(new CellDesignerModificationResidue());
+ CellDesignerSimpleMolecule species = new CellDesignerSimpleMolecule();
+
+ parser.processStateDataInSpecies(species, state);
+ fail("Exception expected");
+ } catch (NotImplementedException e) {
+ assertTrue(e.getMessage().contains("Modification not supported in SimpleMolecule"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testProcessInvalidStateDataInSpecies5() throws Exception {
+ try {
+ SpeciesState state = new SpeciesState();
+ state.setStructuralState("state");
+ CellDesignerSimpleMolecule species = new CellDesignerSimpleMolecule();
+
+ parser.processStateDataInSpecies(species, state);
+ fail("Exception expected");
+ } catch (NotImplementedException e) {
+ assertTrue(e.getMessage().contains("Structural state not supported in SimpleMolecule"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testProcessInvalidStateDataInSpecies6() throws Exception {
+ try {
+ SpeciesState state = new SpeciesState();
+ state.setStructuralState("state");
+ CellDesignerAntisenseRna species = new CellDesignerAntisenseRna();
+
+ parser.processStateDataInSpecies(species, state);
+ fail("Exception expected");
+ } catch (NotImplementedException e) {
+ assertTrue(e.getMessage().contains("Structural state not supported in AntisenseRna"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testProcessInvalidStateDataInSpecies7() throws Exception {
+ try {
+ SpeciesState state = new SpeciesState();
+ state.setStructuralState("state");
+ CellDesignerSpecies<?> species = new CellDesignerSpecies<Gene>();
+
+ parser.processStateDataInSpecies(species, state);
+ fail("Exception expected");
+ } catch (NotImplementedException e) {
+ assertTrue(e.getMessage().contains("Structural state not supported"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testProcessInvalidStateDataInSpecies8() throws Exception {
+ try {
+ SpeciesState state = new SpeciesState();
+ state.addModificationResidue(new CellDesignerModificationResidue());
+ CellDesignerSpecies<?> species = new CellDesignerSpecies<Gene>();
+
+ parser.processStateDataInSpecies(species, state);
+ fail("Exception expected");
+ } catch (NotImplementedException e) {
+ assertTrue(e.getMessage().contains("Modification not supported in"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testProcessAntisenseRnaStateDataInSpecies() throws Exception {
+ try {
+ SpeciesState state = new SpeciesState();
+ state.addModificationResidue(new CellDesignerModificationResidue());
+ CellDesignerAntisenseRna species = new CellDesignerAntisenseRna();
+
+ parser.processStateDataInSpecies(species, state);
+
+ assertEquals(1, species.getRegions().size());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCreateRnaRegion() throws Exception {
+ try {
+ CellDesignerModificationResidue mr = new CellDesignerModificationResidue();
+ mr.setSize(1.0);
+ mr.setAngle(1.0);
+
+ CellDesignerRnaRegion region = parser.createRnaRegion(mr);
+ assertNotNull(region.getPos());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCreateAntisenseRnaRegion() throws Exception {
+ try {
+ CellDesignerModificationResidue mr = new CellDesignerModificationResidue();
+ mr.setSize(1.0);
+ mr.setAngle(1.0);
+
+ CellDesignerAntisenseRnaRegion region = parser.createAntisenseRnaRegion(mr);
+ assertNotNull(region.getPos());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
}
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/SpeciesTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/SpeciesTest.java
index bbc8f26a2fa2badf0232812318b3316138577733..6bf57cf435dd744eda73613d04e1cda723da2f05 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/SpeciesTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/SpeciesTest.java
@@ -11,327 +11,348 @@ import org.junit.After;
import org.junit.Before;
import org.junit.Test;
+import lcsb.mapviewer.common.Configuration;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.common.exception.NotImplementedException;
import lcsb.mapviewer.converter.model.celldesigner.CellDesignerTestFunctions;
import lcsb.mapviewer.model.map.MiriamData;
+import lcsb.mapviewer.model.map.kinetics.SbmlUnitType;
import lcsb.mapviewer.model.map.species.GenericProtein;
import lcsb.mapviewer.model.map.species.Rna;
public class SpeciesTest extends CellDesignerTestFunctions {
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testSerialization() {
- try {
- SerializationUtils.serialize(new CellDesignerSpecies<GenericProtein>());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetters() {
- try {
- CellDesignerSpecies<?> species = new CellDesignerSpecies<GenericProtein>();
- String elementId = "51";
- Integer initialAmount = 54;
- Integer initialConcentration = 58;
- Integer charge = 59;
- Boolean onlySubstanceUnits = true;
-
- String trueStr = "true";
- assertFalse(species.isHypothetical());
- species.setHypothetical(trueStr);
- assertTrue(species.isHypothetical());
-
- species.setElementId(elementId);
- assertEquals(elementId, species.getElementId());
-
- species.setInitialAmount(initialAmount);
- assertEquals(initialAmount, species.getInitialAmount());
-
- species.setOnlySubstanceUnits(onlySubstanceUnits);
- assertEquals(onlySubstanceUnits, species.getOnlySubstanceUnits());
-
- species.setInitialConcentration(initialConcentration);
- assertEquals(initialConcentration, species.getInitialConcentration());
-
- species.setCharge(charge);
-
- assertEquals(charge, species.getCharge());
-
- species.setElementId("");
- assertEquals("", species.getElementId());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testConstructor() {
- try {
- String id = "as_id";
- CellDesignerSpecies<?> species = new CellDesignerSpecies<GenericProtein>(id);
- assertEquals(id, species.getElementId());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testSetId() {
- try {
- CellDesignerSpecies<?> species = new CellDesignerSpecies<GenericProtein>();
- species.setElementId("");
- species.setElementId("xx");
- try {
- species.setElementId("yy");
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
-
- }
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testUpdate1() {
- try {
- int warningsCount = getWarnings().size();
- CellDesignerSpecies<?> species = new CellDesignerSpecies<GenericProtein>();
- species.setName("A");
- species.setNotes("XXX");
- CellDesignerSpecies<?> species2 = new CellDesignerSpecies<GenericProtein>();
- species2.setName("B");
- species.update(species2);
- int warningsCount2 = getWarnings().size();
- assertEquals(1, warningsCount2 - warningsCount);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testUpdate2() {
- try {
- CellDesignerSpecies<?> species = new CellDesignerSpecies<GenericProtein>();
- species.setNotes("XXX");
- CellDesignerSpecies<?> species2 = new CellDesignerSpecies<GenericProtein>();
- species2.addMiriamData(new MiriamData());
- species.update(species2);
- int warningsCount = getWarnings().size();
- assertEquals(0, warningsCount);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testUpdate3() {
- try {
- CellDesignerSpecies<?> species = new CellDesignerSpecies<GenericProtein>();
- species.setNotes("XXX");
- CellDesignerSpecies<?> species2 = new CellDesignerSpecies<GenericProtein>();
- species2.setNotes("xx");
- species.update(species2);
- int warningsCount = getWarnings().size();
- assertEquals(0, warningsCount);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testUpdate4() {
- try {
- CellDesignerSpecies<?> species = new CellDesignerSpecies<GenericProtein>();
- species.setNotes("XX");
- CellDesignerSpecies<?> species2 = new CellDesignerSpecies<GenericProtein>();
- species2.setNotes("xxX");
- species.update(species2);
- int warningsCount = getWarnings().size();
- assertEquals(0, warningsCount);
- assertEquals(3, species.getNotes().length());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testUpdate5() {
- try {
- CellDesignerSpecies<?> species = new CellDesignerSpecies<GenericProtein>();
- species.setNotes("XX");
- CellDesignerSpecies<?> species2 = new CellDesignerSpecies<GenericProtein>();
- species2.setNotes("a as x");
- species2.setHypothetical(true);
- species2.setSymbol("sym");
- species2.setHomodimer(2);
- species.update(species2);
- int warningsCount = getWarnings().size();
- assertEquals(0, warningsCount);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testUpdate6() {
- try {
- CellDesignerSpecies<?> species = new CellDesignerSpecies<GenericProtein>();
- species.setSymbol("sym1");
- species.setFullName("a_sym1");
- CellDesignerSpecies<?> species2 = new CellDesignerSpecies<GenericProtein>();
- species2.setSymbol("sym2");
- species2.setFullName("b_sym1");
- species.update(species2);
- int warningsCount = getWarnings().size();
- assertEquals(2, warningsCount);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testUpdate7() {
- try {
- CellDesignerSpecies<?> species = new CellDesignerSpecies<GenericProtein>();
- CellDesignerSpecies<?> species2 = new CellDesignerSpecies<GenericProtein>();
- species2.addSynonym("syn");
- species2.addFormerSymbol("sym");
- species.update(species2);
- int warningsCount = getWarnings().size();
- assertEquals(0, warningsCount);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testSetInitialAmount() {
- try {
- CellDesignerSpecies<?> species = new CellDesignerSpecies<GenericProtein>();
- species.setInitialAmount("1");
- assertEquals((Integer) 1, species.getInitialAmount());
- try {
- species.setInitialAmount("a1");
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
- }
- species.setInitialAmount("1");
- species.setInitialAmount((String) null);
- assertNull(species.getInitialAmount());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testSetCharge() {
- try {
- CellDesignerSpecies<?> species = new CellDesignerSpecies<GenericProtein>();
- species.setCharge("1");
- assertEquals((Integer) 1, species.getCharge());
- try {
- species.setCharge("a1");
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
- }
- species.setCharge("1");
- species.setCharge((String) null);
- assertNull(species.getCharge());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testSetOnlySubstanceUnits() {
- try {
- CellDesignerSpecies<?> species = new CellDesignerSpecies<GenericProtein>();
- species.setOnlySubstanceUnits("true");
- assertTrue(species.getOnlySubstanceUnits());
- try {
- species.setOnlySubstanceUnits("a1");
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
- }
- species.setOnlySubstanceUnits("false");
- assertFalse(species.getOnlySubstanceUnits());
- species.setOnlySubstanceUnits((String) null);
- assertNull(species.getOnlySubstanceUnits());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testSetInitialConcentration() {
- try {
- CellDesignerSpecies<?> species = new CellDesignerSpecies<GenericProtein>();
- species.setInitialConcentration("1");
- assertEquals((Integer) 1, species.getInitialConcentration());
- try {
- species.setInitialConcentration("a1");
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
- }
- species.setInitialConcentration("1");
- species.setInitialConcentration((String) null);
- assertNull(species.getInitialConcentration());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCreateInvalidElement() {
- try {
- CellDesignerSpecies<?> complex = new CellDesignerSpecies<Rna>();
- complex.createModelElement("id");
- fail("Exception expected");
- } catch (NotImplementedException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testSerialization() {
+ try {
+ SerializationUtils.serialize(new CellDesignerSpecies<GenericProtein>());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetters() {
+ try {
+ CellDesignerSpecies<?> species = new CellDesignerSpecies<GenericProtein>();
+ String elementId = "51";
+ Double initialAmount = 54.0;
+ Double initialConcentration = 58.0;
+ Integer charge = 59;
+ Boolean onlySubstanceUnits = true;
+
+ String trueStr = "true";
+ assertFalse(species.isHypothetical());
+ species.setHypothetical(trueStr);
+ assertTrue(species.isHypothetical());
+
+ species.setElementId(elementId);
+ assertEquals(elementId, species.getElementId());
+
+ species.setInitialAmount(initialAmount);
+ assertEquals(initialAmount, species.getInitialAmount());
+
+ species.setOnlySubstanceUnits(onlySubstanceUnits);
+ assertEquals(onlySubstanceUnits, species.getOnlySubstanceUnits());
+
+ species.setInitialConcentration(initialConcentration);
+ assertEquals(initialConcentration, species.getInitialConcentration());
+
+ species.setCharge(charge);
+
+ assertEquals(charge, species.getCharge());
+
+ species.setElementId("");
+ assertEquals("", species.getElementId());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testConstructor() {
+ try {
+ String id = "as_id";
+ CellDesignerSpecies<?> species = new CellDesignerSpecies<GenericProtein>(id);
+ assertEquals(id, species.getElementId());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCopy() {
+ try {
+ String id = "as_id";
+ CellDesignerSpecies<GenericProtein> species = new CellDesignerSpecies<>(id);
+ species.setBoundaryCondition(true);
+ species.setConstant(true);
+ species.setSubstanceUnits(SbmlUnitType.COULUMB);
+ CellDesignerSpecies<?> copy = species.copy();
+ assertEquals(id, species.getElementId());
+ assertEquals(Boolean.TRUE, copy.isBoundaryCondition());
+ assertEquals(Boolean.TRUE, copy.isConstant());
+ assertEquals(SbmlUnitType.COULUMB, copy.getSubstanceUnit());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testSetId() {
+ try {
+ CellDesignerSpecies<?> species = new CellDesignerSpecies<GenericProtein>();
+ species.setElementId("");
+ species.setElementId("xx");
+ try {
+ species.setElementId("yy");
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+
+ }
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testUpdate1() {
+ try {
+ int warningsCount = getWarnings().size();
+ CellDesignerSpecies<?> species = new CellDesignerSpecies<GenericProtein>();
+ species.setName("A");
+ species.setNotes("XXX");
+ CellDesignerSpecies<?> species2 = new CellDesignerSpecies<GenericProtein>();
+ species2.setName("B");
+ species.update(species2);
+ int warningsCount2 = getWarnings().size();
+ assertEquals(1, warningsCount2 - warningsCount);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testUpdate2() {
+ try {
+ CellDesignerSpecies<?> species = new CellDesignerSpecies<GenericProtein>();
+ species.setNotes("XXX");
+ CellDesignerSpecies<?> species2 = new CellDesignerSpecies<GenericProtein>();
+ species2.addMiriamData(new MiriamData());
+ species.update(species2);
+ int warningsCount = getWarnings().size();
+ assertEquals(0, warningsCount);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testUpdate3() {
+ try {
+ CellDesignerSpecies<?> species = new CellDesignerSpecies<GenericProtein>();
+ species.setNotes("XXX");
+ CellDesignerSpecies<?> species2 = new CellDesignerSpecies<GenericProtein>();
+ species2.setNotes("xx");
+ species.update(species2);
+ int warningsCount = getWarnings().size();
+ assertEquals(0, warningsCount);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testUpdate4() {
+ try {
+ CellDesignerSpecies<?> species = new CellDesignerSpecies<GenericProtein>();
+ species.setNotes("XX");
+ CellDesignerSpecies<?> species2 = new CellDesignerSpecies<GenericProtein>();
+ species2.setNotes("xxX");
+ species.update(species2);
+ int warningsCount = getWarnings().size();
+ assertEquals(0, warningsCount);
+ assertEquals(3, species.getNotes().length());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testUpdate5() {
+ try {
+ CellDesignerSpecies<?> species = new CellDesignerSpecies<GenericProtein>();
+ species.setNotes("XX");
+ CellDesignerSpecies<?> species2 = new CellDesignerSpecies<GenericProtein>();
+ species2.setNotes("a as x");
+ species2.setHypothetical(true);
+ species2.setSymbol("sym");
+ species2.setHomodimer(2);
+ species.update(species2);
+ int warningsCount = getWarnings().size();
+ assertEquals(0, warningsCount);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testUpdate6() {
+ try {
+ CellDesignerSpecies<?> species = new CellDesignerSpecies<GenericProtein>();
+ species.setSymbol("sym1");
+ species.setFullName("a_sym1");
+ CellDesignerSpecies<?> species2 = new CellDesignerSpecies<GenericProtein>();
+ species2.setSymbol("sym2");
+ species2.setFullName("b_sym1");
+ species.update(species2);
+ int warningsCount = getWarnings().size();
+ assertEquals(2, warningsCount);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testUpdate7() {
+ try {
+ CellDesignerSpecies<?> species = new CellDesignerSpecies<GenericProtein>();
+ CellDesignerSpecies<?> species2 = new CellDesignerSpecies<GenericProtein>();
+ species2.addSynonym("syn");
+ species2.addFormerSymbol("sym");
+ species.update(species2);
+ int warningsCount = getWarnings().size();
+ assertEquals(0, warningsCount);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testSetInitialAmount() {
+ try {
+ CellDesignerSpecies<?> species = new CellDesignerSpecies<GenericProtein>();
+ species.setInitialAmount("1");
+ assertEquals(1, species.getInitialAmount(), Configuration.EPSILON);
+ try {
+ species.setInitialAmount("a1");
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+ }
+ species.setInitialAmount("1");
+ species.setInitialAmount((String) null);
+ assertNull(species.getInitialAmount());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testSetCharge() {
+ try {
+ CellDesignerSpecies<?> species = new CellDesignerSpecies<GenericProtein>();
+ species.setCharge("1");
+ assertEquals((Integer) 1, species.getCharge());
+ try {
+ species.setCharge("a1");
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+ }
+ species.setCharge("1");
+ species.setCharge((String) null);
+ assertNull(species.getCharge());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testSetOnlySubstanceUnits() {
+ try {
+ CellDesignerSpecies<?> species = new CellDesignerSpecies<GenericProtein>();
+ species.setOnlySubstanceUnits("true");
+ assertTrue(species.getOnlySubstanceUnits());
+ try {
+ species.setOnlySubstanceUnits("a1");
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+ }
+ species.setOnlySubstanceUnits("false");
+ assertFalse(species.getOnlySubstanceUnits());
+ species.setOnlySubstanceUnits((String) null);
+ assertNull(species.getOnlySubstanceUnits());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testSetInitialConcentration() {
+ try {
+ CellDesignerSpecies<?> species = new CellDesignerSpecies<GenericProtein>();
+ species.setInitialConcentration("1");
+ assertEquals(1, species.getInitialConcentration(), Configuration.EPSILON);
+ try {
+ species.setInitialConcentration("a1");
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+ }
+ species.setInitialConcentration("1");
+ species.setInitialConcentration((String) null);
+ assertNull(species.getInitialConcentration());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCreateInvalidElement() {
+ try {
+ CellDesignerSpecies<?> complex = new CellDesignerSpecies<Rna>();
+ complex.createModelElement("id");
+ fail("Exception expected");
+ } catch (NotImplementedException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
}
diff --git a/converter-CellDesigner/testFiles/elements_with_kinetic_data.xml b/converter-CellDesigner/testFiles/elements_with_kinetic_data.xml
new file mode 100644
index 0000000000000000000000000000000000000000..19cbcdbf58dbd89805b4e9632c35c6037b287510
--- /dev/null
+++ b/converter-CellDesigner/testFiles/elements_with_kinetic_data.xml
@@ -0,0 +1,117 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level2/version4" xmlns:celldesigner="http://www.sbml.org/2001/ns/celldesigner" level="2" version="4">
+<model metaid="untitled" id="untitled">
+<annotation>
+<celldesigner:extension>
+<celldesigner:modelVersion>4.0</celldesigner:modelVersion>
+<celldesigner:modelDisplay sizeX="600" sizeY="400"/>
+<celldesigner:listOfCompartmentAliases/>
+<celldesigner:listOfComplexSpeciesAliases/>
+<celldesigner:listOfSpeciesAliases>
+<celldesigner:speciesAlias id="sa1" species="s1">
+<celldesigner:activity>inactive</celldesigner:activity>
+<celldesigner:bounds x="172.0" y="155.0" w="80.0" h="40.0"/>
+<celldesigner:font size="12"/>
+<celldesigner:view state="usual"/>
+<celldesigner:usualView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="80.0" height="40.0"/>
+<celldesigner:singleLine width="1.0"/>
+<celldesigner:paint color="ffccffcc" scheme="Color"/>
+</celldesigner:usualView>
+<celldesigner:briefView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="80.0" height="60.0"/>
+<celldesigner:singleLine width="0.0"/>
+<celldesigner:paint color="3fff0000" scheme="Color"/>
+</celldesigner:briefView>
+<celldesigner:info state="empty" angle="-1.5707963267948966"/>
+</celldesigner:speciesAlias>
+<celldesigner:speciesAlias id="sa2" species="s2">
+<celldesigner:activity>inactive</celldesigner:activity>
+<celldesigner:bounds x="308.0" y="154.0" w="80.0" h="40.0"/>
+<celldesigner:font size="12"/>
+<celldesigner:view state="usual"/>
+<celldesigner:usualView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="80.0" height="40.0"/>
+<celldesigner:singleLine width="1.0"/>
+<celldesigner:paint color="ffccffcc" scheme="Color"/>
+</celldesigner:usualView>
+<celldesigner:briefView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="80.0" height="60.0"/>
+<celldesigner:singleLine width="0.0"/>
+<celldesigner:paint color="3fff0000" scheme="Color"/>
+</celldesigner:briefView>
+<celldesigner:info state="empty" angle="-1.5707963267948966"/>
+</celldesigner:speciesAlias>
+</celldesigner:listOfSpeciesAliases>
+<celldesigner:listOfGroups/>
+<celldesigner:listOfProteins>
+<celldesigner:protein id="pr1" name="s1" type="GENERIC"/>
+<celldesigner:protein id="pr2" name="s2" type="GENERIC"/>
+</celldesigner:listOfProteins>
+<celldesigner:listOfGenes/>
+<celldesigner:listOfRNAs/>
+<celldesigner:listOfAntisenseRNAs/>
+<celldesigner:listOfLayers/>
+<celldesigner:listOfBlockDiagrams/>
+</celldesigner:extension>
+</annotation>
+<listOfUnitDefinitions>
+<unitDefinition metaid="substance" id="substance" name="substance">
+<listOfUnits>
+<unit metaid="CDMT00001" kind="mole"/>
+</listOfUnits>
+</unitDefinition>
+<unitDefinition metaid="volume" id="volume" name="volume">
+<listOfUnits>
+<unit metaid="CDMT00002" kind="litre"/>
+</listOfUnits>
+</unitDefinition>
+<unitDefinition metaid="area" id="area" name="area">
+<listOfUnits>
+<unit metaid="CDMT00003" kind="metre" exponent="2"/>
+</listOfUnits>
+</unitDefinition>
+<unitDefinition metaid="length" id="length" name="length">
+<listOfUnits>
+<unit metaid="CDMT00004" kind="metre"/>
+</listOfUnits>
+</unitDefinition>
+<unitDefinition metaid="time" id="time" name="time">
+<listOfUnits>
+<unit metaid="CDMT00005" kind="second"/>
+</listOfUnits>
+</unitDefinition>
+</listOfUnitDefinitions>
+<listOfCompartments>
+<compartment metaid="default" id="default" size="1" units="volume"/>
+</listOfCompartments>
+<listOfSpecies>
+<species metaid="s1" id="s1" name="s1" compartment="default" initialAmount="2.5" substanceUnits="gram" hasOnlySubstanceUnits="true" boundaryCondition="true" charge="0" constant="true">
+<annotation>
+<celldesigner:extension>
+<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
+<celldesigner:speciesIdentity>
+<celldesigner:class>PROTEIN</celldesigner:class>
+<celldesigner:proteinReference>pr1</celldesigner:proteinReference>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+</annotation>
+</species>
+<species metaid="s2" id="s2" name="s2" compartment="default" initialConcentration="3.7" substanceUnits="mole" charge="0">
+<annotation>
+<celldesigner:extension>
+<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
+<celldesigner:speciesIdentity>
+<celldesigner:class>PROTEIN</celldesigner:class>
+<celldesigner:proteinReference>pr2</celldesigner:proteinReference>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+</annotation>
+</species>
+</listOfSpecies>
+</model>
+</sbml>
diff --git a/converter-CellDesigner/testFiles/kinetics/species_with_kinetics_param.xml b/converter-CellDesigner/testFiles/kinetics/species_with_kinetics_param.xml
new file mode 100644
index 0000000000000000000000000000000000000000..c518b80d9dfe16058e338208460a784aa44e5710
--- /dev/null
+++ b/converter-CellDesigner/testFiles/kinetics/species_with_kinetics_param.xml
@@ -0,0 +1,11 @@
+<species metaid="s2" id="s2" name="s2" compartment="default" initialConcentration="3.7" substanceUnits="mole" charge="0">
+<annotation>
+<celldesigner:extension>
+<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
+<celldesigner:speciesIdentity>
+<celldesigner:class>PROTEIN</celldesigner:class>
+<celldesigner:proteinReference>pr2</celldesigner:proteinReference>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+</annotation>
+</species>
diff --git a/converter-CellDesigner/testFiles/kinetics/species_with_kinetics_param2.xml b/converter-CellDesigner/testFiles/kinetics/species_with_kinetics_param2.xml
new file mode 100644
index 0000000000000000000000000000000000000000..c83c5c0b21a3659fb30ce323d06b1b9a09c4f6aa
--- /dev/null
+++ b/converter-CellDesigner/testFiles/kinetics/species_with_kinetics_param2.xml
@@ -0,0 +1,11 @@
+<species metaid="s1" id="s1" name="s1" compartment="default" initialAmount="2.5" substanceUnits="gram" hasOnlySubstanceUnits="true" boundaryCondition="true" charge="0" constant="true">
+<annotation>
+<celldesigner:extension>
+<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
+<celldesigner:speciesIdentity>
+<celldesigner:class>PROTEIN</celldesigner:class>
+<celldesigner:proteinReference>pr1</celldesigner:proteinReference>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+</annotation>
+</species>
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/GenericProtein.java b/model/src/main/java/lcsb/mapviewer/model/map/species/GenericProtein.java
index 428c069554b76f5326e73dc1f5832d705447936b..d3b1db81c7e052d1e07fdde67aab58b04b2447d2 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/GenericProtein.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/GenericProtein.java
@@ -15,44 +15,44 @@ import lcsb.mapviewer.common.exception.NotImplementedException;
@DiscriminatorValue("GENERIC_PROTEIN_ALIAS")
public class GenericProtein extends Protein {
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Empty constructor required by hibernate.
- */
- GenericProtein() {
- }
-
- /**
- * Default constructor.
- *
- * @param elementId
- * uniqe (within model) element identifier
- */
- public GenericProtein(String elementId) {
- super(elementId);
- }
-
- /**
- * Constructor that creates a copy of the element given in the parameter.
- *
- * @param original
- * original object that will be used for creating copy
- */
- public GenericProtein(GenericProtein original) {
- super(original);
- }
-
- @Override
- public GenericProtein copy() {
- if (this.getClass() == GenericProtein.class) {
- return new GenericProtein(this);
- } else {
- throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
- }
- }
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Empty constructor required by hibernate.
+ */
+ GenericProtein() {
+ }
+
+ /**
+ * Default constructor.
+ *
+ * @param elementId
+ * unique (within model) element identifier
+ */
+ public GenericProtein(String elementId) {
+ super(elementId);
+ }
+
+ /**
+ * Constructor that creates a copy of the element given in the parameter.
+ *
+ * @param original
+ * original object that will be used for creating copy
+ */
+ public GenericProtein(GenericProtein original) {
+ super(original);
+ }
+
+ @Override
+ public GenericProtein copy() {
+ if (this.getClass() == GenericProtein.class) {
+ return new GenericProtein(this);
+ } else {
+ throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
+ }
+ }
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/Protein.java b/model/src/main/java/lcsb/mapviewer/model/map/species/Protein.java
index 7fadc2e18f348c095c984d176ebb93d2b2a3643a..9e891ddd9df99c9d85a2449c86e9a43128b29295 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/Protein.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/Protein.java
@@ -24,101 +24,102 @@ import lcsb.mapviewer.model.map.species.field.ModificationResidue;
@DiscriminatorValue("PROTEIN_ALIAS")
public abstract class Protein extends Species {
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * State of the protein.
- */
- private String structuralState = null;
-
- /**
- * List of modifications for the Protein.
- */
- @Cascade({ CascadeType.ALL })
- @OneToMany(mappedBy = "species", orphanRemoval = true)
- @LazyCollection(LazyCollectionOption.FALSE)
- private List<ModificationResidue> modificationResidues = new ArrayList<>();
-
- /**
- * Empty constructor required by hibernate.
- */
- Protein() {
- }
-
- /**
- * Constructor that creates a copy of the element given in the parameter.
- *
- * @param original
- * original object that will be used for creating copy
- */
- protected Protein(Protein original) {
- super(original);
- this.structuralState = original.getStructuralState();
- for (ModificationResidue mr : original.getModificationResidues()) {
- addModificationResidue(new ModificationResidue(mr));
- }
- }
-
-
- /**
- * Default constructor.
- *
- * @param elementId
- * uniqe (within model) element identifier
- */
- protected Protein(String elementId) {
- super(elementId);
- }
-
- /**
- * Adds modification to the protein.
- *
- * @param modificationResidue
- * modification to add
- */
- public void addModificationResidue(ModificationResidue modificationResidue) {
- modificationResidues.add(modificationResidue);
- modificationResidue.setSpecies(this);
- }
-
- /**
- * @return the modificationResidues
- * @see #modificationResidues
- */
- public List<ModificationResidue> getModificationResidues() {
- return modificationResidues;
- }
-
- /**
- * @param modificationResidues the modificationResidues to set
- * @see #modificationResidues
- */
- public void setModificationResidues(List<ModificationResidue> modificationResidues) {
- this.modificationResidues = modificationResidues;
- }
-
- /**
- * @return the structuralState
- * @see #structuralState
- */
- public String getStructuralState() {
- return structuralState;
- }
-
- /**
- * @param structuralState the structuralState to set
- * @see #structuralState
- */
- public void setStructuralState(String structuralState) {
- this.structuralState = structuralState;
- }
-
- @Override
- public String getStringType() {
- return "Protein";
- }
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * State of the protein.
+ */
+ private String structuralState = null;
+
+ /**
+ * List of modifications for the Protein.
+ */
+ @Cascade({ CascadeType.ALL })
+ @OneToMany(mappedBy = "species", orphanRemoval = true)
+ @LazyCollection(LazyCollectionOption.FALSE)
+ private List<ModificationResidue> modificationResidues = new ArrayList<>();
+
+ /**
+ * Empty constructor required by hibernate.
+ */
+ Protein() {
+ }
+
+ /**
+ * Constructor that creates a copy of the element given in the parameter.
+ *
+ * @param original
+ * original object that will be used for creating copy
+ */
+ protected Protein(Protein original) {
+ super(original);
+ this.structuralState = original.getStructuralState();
+ for (ModificationResidue mr : original.getModificationResidues()) {
+ addModificationResidue(new ModificationResidue(mr));
+ }
+ }
+
+ /**
+ * Default constructor.
+ *
+ * @param elementId
+ * unique (within model) element identifier
+ */
+ protected Protein(String elementId) {
+ super(elementId);
+ }
+
+ /**
+ * Adds modification to the protein.
+ *
+ * @param modificationResidue
+ * modification to add
+ */
+ public void addModificationResidue(ModificationResidue modificationResidue) {
+ modificationResidues.add(modificationResidue);
+ modificationResidue.setSpecies(this);
+ }
+
+ /**
+ * @return the modificationResidues
+ * @see #modificationResidues
+ */
+ public List<ModificationResidue> getModificationResidues() {
+ return modificationResidues;
+ }
+
+ /**
+ * @param modificationResidues
+ * the modificationResidues to set
+ * @see #modificationResidues
+ */
+ public void setModificationResidues(List<ModificationResidue> modificationResidues) {
+ this.modificationResidues = modificationResidues;
+ }
+
+ /**
+ * @return the structuralState
+ * @see #structuralState
+ */
+ public String getStructuralState() {
+ return structuralState;
+ }
+
+ /**
+ * @param structuralState
+ * the structuralState to set
+ * @see #structuralState
+ */
+ public void setStructuralState(String structuralState) {
+ this.structuralState = structuralState;
+ }
+
+ @Override
+ public String getStringType() {
+ return "Protein";
+ }
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/Species.java b/model/src/main/java/lcsb/mapviewer/model/map/species/Species.java
index f1acb7f47bcdd6dc4fe20a5dcf2898965f189ba6..5f8e2f0b25a71707b272617b7c86e8e7390505ed 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/Species.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/Species.java
@@ -16,6 +16,8 @@ import org.apache.log4j.Logger;
import org.hibernate.annotations.Cascade;
import org.hibernate.annotations.CascadeType;
+import lcsb.mapviewer.model.map.kinetics.SbmlUnit;
+import lcsb.mapviewer.model.map.kinetics.SbmlUnitType;
import lcsb.mapviewer.model.map.species.field.PositionToCompartment;
import lcsb.mapviewer.model.map.species.field.UniprotRecord;
@@ -81,7 +83,7 @@ public abstract class Species extends Element {
/**
* Initial amount of species.
*/
- private Integer initialAmount = null;
+ private Double initialAmount = null;
/**
* Charge of the species.
@@ -91,7 +93,7 @@ public abstract class Species extends Element {
/**
* Initial concentration of species.
*/
- private Integer initialConcentration = null;
+ private Double initialConcentration = null;
/**
* Is only substance units allowed.
@@ -121,6 +123,12 @@ public abstract class Species extends Element {
@OneToMany(fetch = FetchType.EAGER, mappedBy = "species", orphanRemoval = true)
private Set<UniprotRecord> uniprots = new HashSet<>();
+ private Boolean boundaryCondition;
+
+ private Boolean constant;
+
+ private SbmlUnitType substanceUnits;
+
/**
* Constructor that set element identifier.
*
@@ -167,6 +175,9 @@ public abstract class Species extends Element {
homodimer = original.getHomodimer();
positionToCompartment = original.getPositionToCompartment();
hypothetical = original.getHypothetical();
+ boundaryCondition = original.getBoundaryCondition();
+ constant = original.getConstant();
+ substanceUnits = original.getSubstanceUnits();
uniprots = original.getUniprots();
@@ -282,7 +293,7 @@ public abstract class Species extends Element {
* @return the initialAmount
* @see #initialAmount
*/
- public Integer getInitialAmount() {
+ public Double getInitialAmount() {
return initialAmount;
}
@@ -291,7 +302,7 @@ public abstract class Species extends Element {
* the initialAmount to set
* @see #initialAmount
*/
- public void setInitialAmount(Integer initialAmount) {
+ public void setInitialAmount(Double initialAmount) {
this.initialAmount = initialAmount;
}
@@ -316,7 +327,7 @@ public abstract class Species extends Element {
* @return the initialConcentration
* @see #initialConcentration
*/
- public Integer getInitialConcentration() {
+ public Double getInitialConcentration() {
return initialConcentration;
}
@@ -325,7 +336,7 @@ public abstract class Species extends Element {
* the initialConcentration to set
* @see #initialConcentration
*/
- public void setInitialConcentration(Integer initialConcentration) {
+ public void setInitialConcentration(Double initialConcentration) {
this.initialConcentration = initialConcentration;
}
@@ -435,4 +446,42 @@ public abstract class Species extends Element {
return hypothetical;
}
+ public boolean isBoundaryCondition() {
+ if (boundaryCondition == null) {
+ return false;
+ }
+ return boundaryCondition;
+ }
+
+ public Boolean getBoundaryCondition() {
+ return boundaryCondition;
+ }
+
+ public void setBoundaryCondition(Boolean boundaryCondition) {
+ this.boundaryCondition = boundaryCondition;
+ }
+
+ public boolean isConstant() {
+ if (constant == null) {
+ return false;
+ }
+ return constant;
+ }
+
+ public Boolean getConstant() {
+ return constant;
+ }
+
+ public SbmlUnitType getSubstanceUnits() {
+ return substanceUnits;
+ }
+
+ public void setConstant(Boolean constant) {
+ this.constant = constant;
+ }
+
+ public void setSubstanceUnits(SbmlUnitType substanceUnits) {
+ this.substanceUnits = substanceUnits;
+ }
+
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/SpeciesComparator.java b/model/src/main/java/lcsb/mapviewer/model/map/species/SpeciesComparator.java
index c3e6141b3b7c8a617dabd4e661ea7d8cfa2b5b3e..39434f3526dbacd60c944d2d3054d2aa5ef24f6a 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/SpeciesComparator.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/SpeciesComparator.java
@@ -87,9 +87,9 @@ public class SpeciesComparator extends Comparator<Species> {
return stringComparator.compare(arg0.getStatePrefix(), arg1.getStatePrefix());
}
- if (integerComparator.compare(arg0.getInitialAmount(), arg1.getInitialAmount()) != 0) {
+ if (doubleComparator.compare(arg0.getInitialAmount(), arg1.getInitialAmount()) != 0) {
logger.debug("Initial amount different: " + arg0.getInitialAmount() + ", " + arg1.getInitialAmount());
- return integerComparator.compare(arg0.getInitialAmount(), arg1.getInitialAmount());
+ return doubleComparator.compare(arg0.getInitialAmount(), arg1.getInitialAmount());
}
if (integerComparator.compare(arg0.getCharge(), arg1.getCharge()) != 0) {
@@ -102,10 +102,10 @@ public class SpeciesComparator extends Comparator<Species> {
return integerComparator.compare(arg0.getHomodimer(), arg1.getHomodimer());
}
- if (integerComparator.compare(arg0.getInitialConcentration(), arg1.getInitialConcentration()) != 0) {
+ if (doubleComparator.compare(arg0.getInitialConcentration(), arg1.getInitialConcentration()) != 0) {
logger.debug(
"Initial concentration different: " + arg0.getInitialConcentration() + ", " + arg1.getInitialConcentration());
- return integerComparator.compare(arg0.getInitialConcentration(), arg1.getInitialConcentration());
+ return doubleComparator.compare(arg0.getInitialConcentration(), arg1.getInitialConcentration());
}
if (booleanComparator.compare(arg0.hasOnlySubstanceUnits(), arg1.hasOnlySubstanceUnits()) != 0) {
diff --git a/model/src/test/java/lcsb/mapviewer/AllTests.java b/model/src/test/java/lcsb/mapviewer/AllTests.java
index 95fc5378830086cd2232c50cce02ef7ab459c59b..cfbbd296b9afd343f69799326901595767c227c5 100644
--- a/model/src/test/java/lcsb/mapviewer/AllTests.java
+++ b/model/src/test/java/lcsb/mapviewer/AllTests.java
@@ -8,8 +8,8 @@ import org.junit.runners.Suite;
import org.junit.runners.Suite.SuiteClasses;
@RunWith(Suite.class)
-@SuiteClasses({ AllModelTests.class,//
- AllMapUtilTests.class,//
+@SuiteClasses({ AllModelTests.class, //
+ AllMapUtilTests.class,//
})
public class AllTests {
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/species/ElementComparatorTest.java b/model/src/test/java/lcsb/mapviewer/model/map/species/ElementComparatorTest.java
index 7a6bdc24d0d6d341dcc54f14d386f532ac75b869..19058bdb84912d2348935f323bebf8ccbc274d5b 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/species/ElementComparatorTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/species/ElementComparatorTest.java
@@ -27,296 +27,295 @@ import lcsb.mapviewer.model.map.species.field.PositionToCompartment;
public class ElementComparatorTest {
- ElementComparator comparator = new ElementComparator();
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testCompareException() throws Exception {
- try {
- comparator.compare(Mockito.mock(Element.class), Mockito.mock(Element.class));
-
- fail("Exception should occur");
- } catch (NotImplementedException e) {
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testDifferent() throws Exception {
- try {
- assertTrue(comparator.compare(new GenericProtein("id2"), new GenericProtein("id1")) != 0);
-
- assertTrue(comparator.compare(null, new GenericProtein()) != 0);
- assertTrue(comparator.compare(new GenericProtein(), null) != 0);
- assertTrue(comparator.compare(new GenericProtein(), new Complex()) != 0);
-
- Species sa1 = new GenericProtein("id2");
- Species sa2 = new GenericProtein("id2");
- sa2.setX(2);
- assertTrue(comparator.compare(sa1, sa2) != 0);
-
- sa1 = new GenericProtein("id2");
- sa2 = new GenericProtein("id2");
- sa2.setY(2);
- assertTrue(comparator.compare(sa1, sa2) != 0);
-
- sa1 = new GenericProtein("id2");
- sa2 = new GenericProtein("id2");
- sa2.setHeight(2);
- assertTrue(comparator.compare(sa1, sa2) != 0);
-
- sa1 = new GenericProtein("id2");
- sa2 = new GenericProtein("id2");
- sa2.setFontSize(2);
- assertTrue(comparator.compare(sa1, sa2) != 0);
-
- sa1 = new GenericProtein("id2");
- sa2 = new GenericProtein("id2");
- sa2.setColor(Color.BLUE);
- assertTrue(comparator.compare(sa1, sa2) != 0);
-
- sa1 = new GenericProtein("id2");
- sa2 = new GenericProtein("id2");
- sa2.setVisibilityLevel(6);
- assertTrue(comparator.compare(sa1, sa2) != 0);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCompareSubmodel() throws Exception {
- try {
- Element element1 = createElement();
- Element element2 = createElement();
- assertEquals(0, comparator.compare(element1, element2));
-
- element1.setSubmodel(null);
- assertTrue(comparator.compare(element1, element2) != 0);
- assertTrue(comparator.compare(element2, element1) != 0);
-
- element1 = createElement();
- element2 = createElement();
-
- element1.getSubmodel().setName("Na");
-
- assertTrue(comparator.compare(element1, element2) != 0);
- assertTrue(comparator.compare(element2, element1) != 0);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- private Element createElement() {
- Element result = new GenericProtein("id2");
- ElementSubmodelConnection submodel = new ElementSubmodelConnection(getModel(), SubmodelType.DOWNSTREAM_TARGETS);
- result.setSubmodel(submodel);
- return result;
- }
-
- private Model getModel() {
- Model model = new ModelFullIndexed(null);
-
- model.setNotes("Some description");
- GenericProtein protein = new GenericProtein("A");
- protein.setName("ad");
- model.addElement(protein);
-
- Protein protein2 = new GenericProtein("a_id");
- protein2.setName("ad");
- model.addElement(protein2);
-
- model.addElement(new Compartment("default"));
-
- Layer layer = new Layer();
- layer.setName("layer name");
- model.addLayer(layer);
-
- model.addReaction(new Reaction());
- return model;
- }
-
-
- @Test
- public void testException() {
- try {
- Element el = Mockito.mock(Element.class);
- comparator.compare(el, el);
-
- fail("Exception should occur");
- } catch (NotImplementedException e) {
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testInternalCompare() {
- try {
- SimpleMolecule species1 = createSimpleMolecule();
- assertTrue(comparator.internalCompare(species1, null) != 0);
- assertTrue(comparator.internalCompare(null, species1) != 0);
-
- assertEquals(0, comparator.internalCompare(null, null));
-
- } catch (InvalidClassException e) {
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testDifferent2() {
- try {
- SimpleMolecule species1 = createSimpleMolecule();
- SimpleMolecule species2 = createSimpleMolecule();
-
- species1.setCharge(99);
- assertTrue(comparator.compare(species1, species2) != 0);
- assertTrue(comparator.compare(species2, species1) != 0);
-
- species1 = createSimpleMolecule();
- species2 = createSimpleMolecule();
- species1.setHomodimer(233);
- assertTrue(comparator.compare(species1, species2) != 0);
- assertTrue(comparator.compare(species2, species1) != 0);
-
- species1 = createSimpleMolecule();
- species2 = createSimpleMolecule();
- species1.setFormula("a");
- assertTrue(comparator.compare(species1, species2) != 0);
- assertTrue(comparator.compare(species2, species1) != 0);
-
- species1 = createSimpleMolecule();
- species2 = createSimpleMolecule();
- species1.setElementId("");
- species1.setElementId("ASD");
- assertTrue(comparator.compare(species1, species2) != 0);
- assertTrue(comparator.compare(species2, species1) != 0);
-
- species1 = createSimpleMolecule();
- species2 = createSimpleMolecule();
- species1.setNotes("ASD");
- assertTrue(comparator.compare(species1, species2) != 0);
- assertTrue(comparator.compare(species2, species1) != 0);
-
- species1 = createSimpleMolecule();
- species2 = createSimpleMolecule();
- species1.setPositionToCompartment(PositionToCompartment.INSIDE);
- assertTrue(comparator.compare(species1, species2) != 0);
- assertTrue(comparator.compare(species2, species1) != 0);
-
- species1 = createSimpleMolecule();
- species2 = createSimpleMolecule();
- species1.getMiriamData().clear();
- assertTrue(comparator.compare(species1, species2) != 0);
- assertTrue(comparator.compare(species2, species1) != 0);
-
- species1 = createSimpleMolecule();
- species2 = createSimpleMolecule();
- species1.getMiriamData().iterator().next().setRelationType(MiriamRelationType.BQ_BIOL_HAS_PART);
- assertTrue(comparator.compare(species1, species2) != 0);
- assertTrue(comparator.compare(species2, species1) != 0);
-
- species1 = createSimpleMolecule();
- species2 = createSimpleMolecule();
- species1.addMiriamData(new MiriamData());
- assertTrue(comparator.compare(species1, species2) != 0);
- assertTrue(comparator.compare(species2, species1) != 0);
-
- assertTrue(comparator.compare(species1, null) != 0);
- assertTrue(comparator.compare(null, species1) != 0);
-
- } catch (Exception e) {
- e.printStackTrace();
- fail("Unkowne exception");
- }
- }
-
- @Test
- public void testDifferentNewFields() throws Exception {
- try {
- SimpleMolecule species1 = createSimpleMolecule();
- SimpleMolecule species2 = createSimpleMolecule();
-
- species1.setSymbol("some symbol");
- assertTrue(comparator.compare(species1, species2) != 0);
- assertTrue(comparator.compare(species2, species1) != 0);
-
- species1 = createSimpleMolecule();
- species2 = createSimpleMolecule();
-
- species1.setFullName("some symbol");
- assertTrue(comparator.compare(species1, species2) != 0);
- assertTrue(comparator.compare(species2, species1) != 0);
-
- species1 = createSimpleMolecule();
- species2 = createSimpleMolecule();
-
- species1.getSynonyms().add("asd");
- assertTrue(comparator.compare(species1, species2) != 0);
- assertTrue(comparator.compare(species2, species1) != 0);
-
- species1 = createSimpleMolecule();
- species2 = createSimpleMolecule();
-
- species1.getFormerSymbols().add("asd");
- assertTrue(comparator.compare(species1, species2) != 0);
- assertTrue(comparator.compare(species2, species1) != 0);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- public SimpleMolecule createSimpleMolecule() {
- SimpleMolecule result = new SimpleMolecule("id");
- result.setHomodimer(12);
- result.setName("id");
- result.setInitialAmount(12);
- result.setCharge(13);
- result.setInitialConcentration(14);
- result.setOnlySubstanceUnits(true);
- result.setPositionToCompartment(PositionToCompartment.TRANSMEMBRANE);
- result.setNotes("id");
- MiriamData md = new MiriamData(MiriamRelationType.BQ_BIOL_IS_DESCRIBED_BY, MiriamType.PUBMED, "c");
- result.addMiriamData(md);
- return result;
- }
-
- @Test
- public void testDifferentNewReconFields() throws Exception {
- try {
- SimpleMolecule element1 = createSimpleMolecule();
-
- SimpleMolecule element2 = createSimpleMolecule();
- element2.setAbbreviation("ABRR");
-
- assertTrue(comparator.compare(element1, element2) != 0);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
+ ElementComparator comparator = new ElementComparator();
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testCompareException() throws Exception {
+ try {
+ comparator.compare(Mockito.mock(Element.class), Mockito.mock(Element.class));
+
+ fail("Exception should occur");
+ } catch (NotImplementedException e) {
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testDifferent() throws Exception {
+ try {
+ assertTrue(comparator.compare(new GenericProtein("id2"), new GenericProtein("id1")) != 0);
+
+ assertTrue(comparator.compare(null, new GenericProtein()) != 0);
+ assertTrue(comparator.compare(new GenericProtein(), null) != 0);
+ assertTrue(comparator.compare(new GenericProtein(), new Complex()) != 0);
+
+ Species sa1 = new GenericProtein("id2");
+ Species sa2 = new GenericProtein("id2");
+ sa2.setX(2);
+ assertTrue(comparator.compare(sa1, sa2) != 0);
+
+ sa1 = new GenericProtein("id2");
+ sa2 = new GenericProtein("id2");
+ sa2.setY(2);
+ assertTrue(comparator.compare(sa1, sa2) != 0);
+
+ sa1 = new GenericProtein("id2");
+ sa2 = new GenericProtein("id2");
+ sa2.setHeight(2);
+ assertTrue(comparator.compare(sa1, sa2) != 0);
+
+ sa1 = new GenericProtein("id2");
+ sa2 = new GenericProtein("id2");
+ sa2.setFontSize(2);
+ assertTrue(comparator.compare(sa1, sa2) != 0);
+
+ sa1 = new GenericProtein("id2");
+ sa2 = new GenericProtein("id2");
+ sa2.setColor(Color.BLUE);
+ assertTrue(comparator.compare(sa1, sa2) != 0);
+
+ sa1 = new GenericProtein("id2");
+ sa2 = new GenericProtein("id2");
+ sa2.setVisibilityLevel(6);
+ assertTrue(comparator.compare(sa1, sa2) != 0);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCompareSubmodel() throws Exception {
+ try {
+ Element element1 = createElement();
+ Element element2 = createElement();
+ assertEquals(0, comparator.compare(element1, element2));
+
+ element1.setSubmodel(null);
+ assertTrue(comparator.compare(element1, element2) != 0);
+ assertTrue(comparator.compare(element2, element1) != 0);
+
+ element1 = createElement();
+ element2 = createElement();
+
+ element1.getSubmodel().setName("Na");
+
+ assertTrue(comparator.compare(element1, element2) != 0);
+ assertTrue(comparator.compare(element2, element1) != 0);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ private Element createElement() {
+ Element result = new GenericProtein("id2");
+ ElementSubmodelConnection submodel = new ElementSubmodelConnection(getModel(), SubmodelType.DOWNSTREAM_TARGETS);
+ result.setSubmodel(submodel);
+ return result;
+ }
+
+ private Model getModel() {
+ Model model = new ModelFullIndexed(null);
+
+ model.setNotes("Some description");
+ GenericProtein protein = new GenericProtein("A");
+ protein.setName("ad");
+ model.addElement(protein);
+
+ Protein protein2 = new GenericProtein("a_id");
+ protein2.setName("ad");
+ model.addElement(protein2);
+
+ model.addElement(new Compartment("default"));
+
+ Layer layer = new Layer();
+ layer.setName("layer name");
+ model.addLayer(layer);
+
+ model.addReaction(new Reaction());
+ return model;
+ }
+
+ @Test
+ public void testException() {
+ try {
+ Element el = Mockito.mock(Element.class);
+ comparator.compare(el, el);
+
+ fail("Exception should occur");
+ } catch (NotImplementedException e) {
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testInternalCompare() {
+ try {
+ SimpleMolecule species1 = createSimpleMolecule();
+ assertTrue(comparator.internalCompare(species1, null) != 0);
+ assertTrue(comparator.internalCompare(null, species1) != 0);
+
+ assertEquals(0, comparator.internalCompare(null, null));
+
+ } catch (InvalidClassException e) {
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testDifferent2() {
+ try {
+ SimpleMolecule species1 = createSimpleMolecule();
+ SimpleMolecule species2 = createSimpleMolecule();
+
+ species1.setCharge(99);
+ assertTrue(comparator.compare(species1, species2) != 0);
+ assertTrue(comparator.compare(species2, species1) != 0);
+
+ species1 = createSimpleMolecule();
+ species2 = createSimpleMolecule();
+ species1.setHomodimer(233);
+ assertTrue(comparator.compare(species1, species2) != 0);
+ assertTrue(comparator.compare(species2, species1) != 0);
+
+ species1 = createSimpleMolecule();
+ species2 = createSimpleMolecule();
+ species1.setFormula("a");
+ assertTrue(comparator.compare(species1, species2) != 0);
+ assertTrue(comparator.compare(species2, species1) != 0);
+
+ species1 = createSimpleMolecule();
+ species2 = createSimpleMolecule();
+ species1.setElementId("");
+ species1.setElementId("ASD");
+ assertTrue(comparator.compare(species1, species2) != 0);
+ assertTrue(comparator.compare(species2, species1) != 0);
+
+ species1 = createSimpleMolecule();
+ species2 = createSimpleMolecule();
+ species1.setNotes("ASD");
+ assertTrue(comparator.compare(species1, species2) != 0);
+ assertTrue(comparator.compare(species2, species1) != 0);
+
+ species1 = createSimpleMolecule();
+ species2 = createSimpleMolecule();
+ species1.setPositionToCompartment(PositionToCompartment.INSIDE);
+ assertTrue(comparator.compare(species1, species2) != 0);
+ assertTrue(comparator.compare(species2, species1) != 0);
+
+ species1 = createSimpleMolecule();
+ species2 = createSimpleMolecule();
+ species1.getMiriamData().clear();
+ assertTrue(comparator.compare(species1, species2) != 0);
+ assertTrue(comparator.compare(species2, species1) != 0);
+
+ species1 = createSimpleMolecule();
+ species2 = createSimpleMolecule();
+ species1.getMiriamData().iterator().next().setRelationType(MiriamRelationType.BQ_BIOL_HAS_PART);
+ assertTrue(comparator.compare(species1, species2) != 0);
+ assertTrue(comparator.compare(species2, species1) != 0);
+
+ species1 = createSimpleMolecule();
+ species2 = createSimpleMolecule();
+ species1.addMiriamData(new MiriamData());
+ assertTrue(comparator.compare(species1, species2) != 0);
+ assertTrue(comparator.compare(species2, species1) != 0);
+
+ assertTrue(comparator.compare(species1, null) != 0);
+ assertTrue(comparator.compare(null, species1) != 0);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ fail("Unkowne exception");
+ }
+ }
+
+ @Test
+ public void testDifferentNewFields() throws Exception {
+ try {
+ SimpleMolecule species1 = createSimpleMolecule();
+ SimpleMolecule species2 = createSimpleMolecule();
+
+ species1.setSymbol("some symbol");
+ assertTrue(comparator.compare(species1, species2) != 0);
+ assertTrue(comparator.compare(species2, species1) != 0);
+
+ species1 = createSimpleMolecule();
+ species2 = createSimpleMolecule();
+
+ species1.setFullName("some symbol");
+ assertTrue(comparator.compare(species1, species2) != 0);
+ assertTrue(comparator.compare(species2, species1) != 0);
+
+ species1 = createSimpleMolecule();
+ species2 = createSimpleMolecule();
+
+ species1.getSynonyms().add("asd");
+ assertTrue(comparator.compare(species1, species2) != 0);
+ assertTrue(comparator.compare(species2, species1) != 0);
+
+ species1 = createSimpleMolecule();
+ species2 = createSimpleMolecule();
+
+ species1.getFormerSymbols().add("asd");
+ assertTrue(comparator.compare(species1, species2) != 0);
+ assertTrue(comparator.compare(species2, species1) != 0);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ public SimpleMolecule createSimpleMolecule() {
+ SimpleMolecule result = new SimpleMolecule("id");
+ result.setHomodimer(12);
+ result.setName("id");
+ result.setInitialAmount(12.0);
+ result.setCharge(13);
+ result.setInitialConcentration(14.0);
+ result.setOnlySubstanceUnits(true);
+ result.setPositionToCompartment(PositionToCompartment.TRANSMEMBRANE);
+ result.setNotes("id");
+ MiriamData md = new MiriamData(MiriamRelationType.BQ_BIOL_IS_DESCRIBED_BY, MiriamType.PUBMED, "c");
+ result.addMiriamData(md);
+ return result;
+ }
+
+ @Test
+ public void testDifferentNewReconFields() throws Exception {
+ try {
+ SimpleMolecule element1 = createSimpleMolecule();
+
+ SimpleMolecule element2 = createSimpleMolecule();
+ element2.setAbbreviation("ABRR");
+
+ assertTrue(comparator.compare(element1, element2) != 0);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/species/SpeciesComparatorTest.java b/model/src/test/java/lcsb/mapviewer/model/map/species/SpeciesComparatorTest.java
index 68c0c063dab9fe368b8e8c708ca1778266f6e8a8..869efc203a3383e76b9cf9f1563f2c35a1f40be7 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/species/SpeciesComparatorTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/species/SpeciesComparatorTest.java
@@ -19,270 +19,270 @@ import lcsb.mapviewer.model.map.species.field.PositionToCompartment;
public class SpeciesComparatorTest {
- SpeciesComparator comparator = new SpeciesComparator();
+ SpeciesComparator comparator = new SpeciesComparator();
- @Before
- public void setUp() throws Exception {
- }
+ @Before
+ public void setUp() throws Exception {
+ }
- @After
- public void tearDown() throws Exception {
- }
+ @After
+ public void tearDown() throws Exception {
+ }
- @Test
- public void testEquals() {
- try {
- Species species1 = createSpecies();
- Species species2 = createSpecies();
+ @Test
+ public void testEquals() {
+ try {
+ Species species1 = createSpecies();
+ Species species2 = createSpecies();
- assertEquals(0, comparator.compare(species1, species2));
+ assertEquals(0, comparator.compare(species1, species2));
- assertEquals(0, comparator.compare(null, null));
+ assertEquals(0, comparator.compare(null, null));
- assertEquals(0, comparator.compare(new Complex(), new Complex()));
+ assertEquals(0, comparator.compare(new Complex(), new Complex()));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
- @Test
- public void testCompareInvalid() {
- try {
+ @Test
+ public void testCompareInvalid() {
+ try {
- Species speciesMock = Mockito.mock(Species.class);
- comparator.compare(speciesMock, speciesMock);
- fail("Exception expected");
+ Species speciesMock = Mockito.mock(Species.class);
+ comparator.compare(speciesMock, speciesMock);
+ fail("Exception expected");
- } catch (NotImplementedException e) {
- } catch (Exception e) {
- e.printStackTrace();
- fail("Unkowne exception");
- }
- }
+ } catch (NotImplementedException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ fail("Unkowne exception");
+ }
+ }
- private Species createSpecies() {
- GenericProtein result = new GenericProtein();
- result.setName("a");
+ private Species createSpecies() {
+ GenericProtein result = new GenericProtein();
+ result.setName("a");
- result.setElementId("asd");
- result.setX(12.0);
- result.setY(123.0);
- result.setWidth(4);
- result.setHeight(5);
- result.setFontSize(9.0);
- result.setColor(Color.BLUE);
- result.setVisibilityLevel(14);
- result.setStateLabel("123");
- result.setStatePrefix("1234");
+ result.setElementId("asd");
+ result.setX(12.0);
+ result.setY(123.0);
+ result.setWidth(4);
+ result.setHeight(5);
+ result.setFontSize(9.0);
+ result.setColor(Color.BLUE);
+ result.setVisibilityLevel(14);
+ result.setStateLabel("123");
+ result.setStatePrefix("1234");
- return result;
- }
+ return result;
+ }
- @Test
- public void testDifferent() throws Exception {
- try {
- Species species1 = createSpecies();
- Species species2 = createSpecies();
+ @Test
+ public void testDifferent() throws Exception {
+ try {
+ Species species1 = createSpecies();
+ Species species2 = createSpecies();
- assertTrue(comparator.compare(species1, null) != 0);
- assertTrue(comparator.compare(null, species1) != 0);
+ assertTrue(comparator.compare(species1, null) != 0);
+ assertTrue(comparator.compare(null, species1) != 0);
- assertTrue(comparator.compare(new Complex(), species1) != 0);
+ assertTrue(comparator.compare(new Complex(), species1) != 0);
- species1 = createSpecies();
- species2 = createSpecies();
+ species1 = createSpecies();
+ species2 = createSpecies();
- species1.setElementId("tmp");
+ species1.setElementId("tmp");
- assertTrue(comparator.compare(species1, species2) != 0);
- assertTrue(comparator.compare(species2, species1) != 0);
+ assertTrue(comparator.compare(species1, species2) != 0);
+ assertTrue(comparator.compare(species2, species1) != 0);
- species1 = createSpecies();
- species2 = createSpecies();
+ species1 = createSpecies();
+ species2 = createSpecies();
- species1.setStateLabel("tmp");
+ species1.setStateLabel("tmp");
- assertTrue(comparator.compare(species1, species2) != 0);
- assertTrue(comparator.compare(species2, species1) != 0);
+ assertTrue(comparator.compare(species1, species2) != 0);
+ assertTrue(comparator.compare(species2, species1) != 0);
- species1 = createSpecies();
- species2 = createSpecies();
+ species1 = createSpecies();
+ species2 = createSpecies();
- species1.setStatePrefix("tmp");
-
- assertTrue(comparator.compare(species1, species2) != 0);
- assertTrue(comparator.compare(species2, species1) != 0);
-
- species1 = createSpecies();
- species2 = createSpecies();
-
- species1.setName("new namne");
-
- assertTrue(comparator.compare(species1, species2) != 0);
- assertTrue(comparator.compare(species2, species1) != 0);
-
- species1 = createSpecies();
- species2 = createSpecies();
-
- species1.setActivity(true);
-
- assertTrue(comparator.compare(species1, species2) != 0);
- assertTrue(comparator.compare(species2, species1) != 0);
-
- species1 = createSpecies();
- species2 = createSpecies();
-
- species1.setLineWidth(453.75);
-
- assertTrue(comparator.compare(species1, species2) != 0);
- assertTrue(comparator.compare(species2, species1) != 0);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testException() {
- try {
- Species mock = Mockito.mock(Species.class);
- comparator.compare(mock, mock);
-
- fail("Exception expected");
- } catch (NotImplementedException e) {
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testEquals2() {
- try {
- SimpleMolecule species1 = createSimpleMolecule();
- SimpleMolecule species2 = createSimpleMolecule();
- assertEquals(0, comparator.compare(species1, species2));
-
- assertEquals(0, comparator.compare(null, null));
-
- assertEquals(0, comparator.compare(new AntisenseRna(), new AntisenseRna()));
- assertEquals(0, comparator.compare(new Degraded(), new Degraded()));
- assertEquals(0, comparator.compare(new Drug(), new Drug()));
- assertEquals(0, comparator.compare(new Ion(), new Ion()));
- assertEquals(0, comparator.compare(new Phenotype(), new Phenotype()));
- assertEquals(0, comparator.compare(new Rna(), new Rna()));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testDifferent2() {
- try {
- SimpleMolecule species1 = createSimpleMolecule();
- SimpleMolecule species2 = createSimpleMolecule();
-
- species1.setCharge(99);
- assertTrue(comparator.compare(species1, species2) != 0);
- assertTrue(comparator.compare(species2, species1) != 0);
- assertTrue(comparator.compare(null, species1) != 0);
- assertTrue(comparator.compare(species1, null) != 0);
-
- species1 = createSimpleMolecule();
- species2 = createSimpleMolecule();
- species1.setHomodimer(1233);
- assertTrue(comparator.compare(species1, species2) != 0);
- assertTrue(comparator.compare(species2, species1) != 0);
-
- species1 = createSimpleMolecule();
- species2 = createSimpleMolecule();
- species1.setElementId("");
- species1.setElementId("ASD");
- assertTrue(comparator.compare(species1, species2) != 0);
- assertTrue(comparator.compare(species2, species1) != 0);
-
- species1 = createSimpleMolecule();
- species2 = createSimpleMolecule();
- species1.setNotes("ASD");
- assertTrue(comparator.compare(species1, species2) != 0);
- assertTrue(comparator.compare(species2, species1) != 0);
-
- species1 = createSimpleMolecule();
- species2 = createSimpleMolecule();
- species1.setPositionToCompartment(PositionToCompartment.TRANSMEMBRANE);
- assertTrue(comparator.compare(species1, species2) != 0);
- assertTrue(comparator.compare(species2, species1) != 0);
-
- species1 = createSimpleMolecule();
- species2 = createSimpleMolecule();
- species1.getMiriamData().clear();
- assertTrue(comparator.compare(species1, species2) != 0);
- assertTrue(comparator.compare(species2, species1) != 0);
-
- species1 = createSimpleMolecule();
- species2 = createSimpleMolecule();
- species1.setInitialAmount(4);
- assertTrue(comparator.compare(species1, species2) != 0);
- assertTrue(comparator.compare(species2, species1) != 0);
-
- species1 = createSimpleMolecule();
- species2 = createSimpleMolecule();
- species1.setInitialConcentration(4);
- assertTrue(comparator.compare(species1, species2) != 0);
- assertTrue(comparator.compare(species2, species1) != 0);
-
- species1 = createSimpleMolecule();
- species2 = createSimpleMolecule();
- species1.setOnlySubstanceUnits(false);
- assertTrue(comparator.compare(species1, species2) != 0);
- assertTrue(comparator.compare(species2, species1) != 0);
-
- species1 = createSimpleMolecule();
- species2 = createSimpleMolecule();
- species1.setHypothetical(true);
- assertTrue(comparator.compare(species1, species2) != 0);
- assertTrue(comparator.compare(species2, species1) != 0);
-
- species1 = createSimpleMolecule();
- species2 = createSimpleMolecule();
- species1.getMiriamData().iterator().next().setRelationType(MiriamRelationType.BQ_BIOL_IS);
- assertTrue(comparator.compare(species1, species2) != 0);
- assertTrue(comparator.compare(species2, species1) != 0);
-
- species1 = createSimpleMolecule();
- species2 = createSimpleMolecule();
- species1.addMiriamData(new MiriamData());
- assertTrue(comparator.compare(species1, species2) != 0);
- assertTrue(comparator.compare(species2, species1) != 0);
-
- assertTrue(comparator.compare(new Rna(), new Drug()) != 0);
-
- } catch (Exception e) {
- e.printStackTrace();
- fail("Unkowne exception");
- }
- }
-
- public SimpleMolecule createSimpleMolecule() {
- SimpleMolecule result = new SimpleMolecule();
- result.setHomodimer(12);
- result.setElementId("id");
- result.setName("id");
- result.setInitialAmount(12);
- result.setCharge(13);
- result.setInitialConcentration(14);
- result.setOnlySubstanceUnits(true);
- result.setPositionToCompartment(PositionToCompartment.INSIDE);
- result.setNotes("id");
- MiriamData md = new MiriamData(MiriamRelationType.BQ_BIOL_IS_DESCRIBED_BY, MiriamType.UNKNOWN, "c");
- result.addMiriamData(md);
- return result;
- }
+ species1.setStatePrefix("tmp");
+
+ assertTrue(comparator.compare(species1, species2) != 0);
+ assertTrue(comparator.compare(species2, species1) != 0);
+
+ species1 = createSpecies();
+ species2 = createSpecies();
+
+ species1.setName("new namne");
+
+ assertTrue(comparator.compare(species1, species2) != 0);
+ assertTrue(comparator.compare(species2, species1) != 0);
+
+ species1 = createSpecies();
+ species2 = createSpecies();
+
+ species1.setActivity(true);
+
+ assertTrue(comparator.compare(species1, species2) != 0);
+ assertTrue(comparator.compare(species2, species1) != 0);
+
+ species1 = createSpecies();
+ species2 = createSpecies();
+
+ species1.setLineWidth(453.75);
+
+ assertTrue(comparator.compare(species1, species2) != 0);
+ assertTrue(comparator.compare(species2, species1) != 0);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testException() {
+ try {
+ Species mock = Mockito.mock(Species.class);
+ comparator.compare(mock, mock);
+
+ fail("Exception expected");
+ } catch (NotImplementedException e) {
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testEquals2() {
+ try {
+ SimpleMolecule species1 = createSimpleMolecule();
+ SimpleMolecule species2 = createSimpleMolecule();
+ assertEquals(0, comparator.compare(species1, species2));
+
+ assertEquals(0, comparator.compare(null, null));
+
+ assertEquals(0, comparator.compare(new AntisenseRna(), new AntisenseRna()));
+ assertEquals(0, comparator.compare(new Degraded(), new Degraded()));
+ assertEquals(0, comparator.compare(new Drug(), new Drug()));
+ assertEquals(0, comparator.compare(new Ion(), new Ion()));
+ assertEquals(0, comparator.compare(new Phenotype(), new Phenotype()));
+ assertEquals(0, comparator.compare(new Rna(), new Rna()));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testDifferent2() {
+ try {
+ SimpleMolecule species1 = createSimpleMolecule();
+ SimpleMolecule species2 = createSimpleMolecule();
+
+ species1.setCharge(99);
+ assertTrue(comparator.compare(species1, species2) != 0);
+ assertTrue(comparator.compare(species2, species1) != 0);
+ assertTrue(comparator.compare(null, species1) != 0);
+ assertTrue(comparator.compare(species1, null) != 0);
+
+ species1 = createSimpleMolecule();
+ species2 = createSimpleMolecule();
+ species1.setHomodimer(1233);
+ assertTrue(comparator.compare(species1, species2) != 0);
+ assertTrue(comparator.compare(species2, species1) != 0);
+
+ species1 = createSimpleMolecule();
+ species2 = createSimpleMolecule();
+ species1.setElementId("");
+ species1.setElementId("ASD");
+ assertTrue(comparator.compare(species1, species2) != 0);
+ assertTrue(comparator.compare(species2, species1) != 0);
+
+ species1 = createSimpleMolecule();
+ species2 = createSimpleMolecule();
+ species1.setNotes("ASD");
+ assertTrue(comparator.compare(species1, species2) != 0);
+ assertTrue(comparator.compare(species2, species1) != 0);
+
+ species1 = createSimpleMolecule();
+ species2 = createSimpleMolecule();
+ species1.setPositionToCompartment(PositionToCompartment.TRANSMEMBRANE);
+ assertTrue(comparator.compare(species1, species2) != 0);
+ assertTrue(comparator.compare(species2, species1) != 0);
+
+ species1 = createSimpleMolecule();
+ species2 = createSimpleMolecule();
+ species1.getMiriamData().clear();
+ assertTrue(comparator.compare(species1, species2) != 0);
+ assertTrue(comparator.compare(species2, species1) != 0);
+
+ species1 = createSimpleMolecule();
+ species2 = createSimpleMolecule();
+ species1.setInitialAmount(4.0);
+ assertTrue(comparator.compare(species1, species2) != 0);
+ assertTrue(comparator.compare(species2, species1) != 0);
+
+ species1 = createSimpleMolecule();
+ species2 = createSimpleMolecule();
+ species1.setInitialConcentration(4.0);
+ assertTrue(comparator.compare(species1, species2) != 0);
+ assertTrue(comparator.compare(species2, species1) != 0);
+
+ species1 = createSimpleMolecule();
+ species2 = createSimpleMolecule();
+ species1.setOnlySubstanceUnits(false);
+ assertTrue(comparator.compare(species1, species2) != 0);
+ assertTrue(comparator.compare(species2, species1) != 0);
+
+ species1 = createSimpleMolecule();
+ species2 = createSimpleMolecule();
+ species1.setHypothetical(true);
+ assertTrue(comparator.compare(species1, species2) != 0);
+ assertTrue(comparator.compare(species2, species1) != 0);
+
+ species1 = createSimpleMolecule();
+ species2 = createSimpleMolecule();
+ species1.getMiriamData().iterator().next().setRelationType(MiriamRelationType.BQ_BIOL_IS);
+ assertTrue(comparator.compare(species1, species2) != 0);
+ assertTrue(comparator.compare(species2, species1) != 0);
+
+ species1 = createSimpleMolecule();
+ species2 = createSimpleMolecule();
+ species1.addMiriamData(new MiriamData());
+ assertTrue(comparator.compare(species1, species2) != 0);
+ assertTrue(comparator.compare(species2, species1) != 0);
+
+ assertTrue(comparator.compare(new Rna(), new Drug()) != 0);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ fail("Unkowne exception");
+ }
+ }
+
+ public SimpleMolecule createSimpleMolecule() {
+ SimpleMolecule result = new SimpleMolecule();
+ result.setHomodimer(12);
+ result.setElementId("id");
+ result.setName("id");
+ result.setInitialAmount(12.0);
+ result.setCharge(13);
+ result.setInitialConcentration(14.0);
+ result.setOnlySubstanceUnits(true);
+ result.setPositionToCompartment(PositionToCompartment.INSIDE);
+ result.setNotes("id");
+ MiriamData md = new MiriamData(MiriamRelationType.BQ_BIOL_IS_DESCRIBED_BY, MiriamType.UNKNOWN, "c");
+ result.addMiriamData(md);
+ return result;
+ }
}
diff --git a/persist/src/test/java/lcsb/mapviewer/persist/dao/map/layout/alias/AliasDaoTest2.java b/persist/src/test/java/lcsb/mapviewer/persist/dao/map/layout/alias/AliasDaoTest2.java
index 07af12f8031e03b52279f429e99ffad42999dac4..1aefeefe0383b3e6b860bbe77ab348f73461bc50 100644
--- a/persist/src/test/java/lcsb/mapviewer/persist/dao/map/layout/alias/AliasDaoTest2.java
+++ b/persist/src/test/java/lcsb/mapviewer/persist/dao/map/layout/alias/AliasDaoTest2.java
@@ -29,283 +29,283 @@ import lcsb.mapviewer.model.map.species.field.RnaRegion;
import lcsb.mapviewer.persist.PersistTestFunctions;
public class AliasDaoTest2 extends PersistTestFunctions {
- static Logger logger = Logger.getLogger(AliasDaoTest.class);
-
- private Integer testChargeVal = 1;
- private String testIdAlias = "a";
- private Integer testInitialAmount = 2;
- private Integer testInitialConcentration = 3;
- private String testName = "d";
- private String testNotes = "e";
- private Boolean testOnlySubstanceunits = true;
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testAdd() throws Exception {
- try {
-
- GenericProtein sp = new GenericProtein(testIdAlias);
- sp.setCharge(testChargeVal);
- sp.setInitialAmount(testInitialAmount);
- sp.setInitialConcentration(testInitialConcentration);
- sp.setName(testName);
- sp.setNotes(testNotes);
- sp.setOnlySubstanceUnits(testOnlySubstanceunits);
-
- Compartment parent = new Compartment("comp id");
- sp.setCompartment(parent);
-
- MiriamData md = new MiriamData(MiriamRelationType.BQ_BIOL_IS_DESCRIBED_BY, MiriamType.UNKNOWN, "c");
- sp.addMiriamData(md);
-
- aliasDao.add(sp);
-
- Species sp2 = (Species) aliasDao.getById(sp.getId());
- assertNotNull(sp2);
- assertEquals(sp.getCharge(), sp2.getCharge());
- assertEquals(sp.getElementId(), sp2.getElementId());
- assertEquals(sp.getInitialAmount(), sp2.getInitialAmount());
- assertEquals(sp.getInitialConcentration(), sp2.getInitialConcentration());
- assertEquals(sp.getName(), sp2.getName());
- assertEquals(sp.getNotes(), sp2.getNotes());
- assertEquals(sp.hasOnlySubstanceUnits(), sp2.hasOnlySubstanceUnits());
-
- Compartment parent2 = sp2.getCompartment();
- assertNotNull(parent2);
- assertEquals("comp id", parent2.getElementId());
-
- assertNotNull(sp2.getMiriamData());
-
- MiriamData md2 = sp2.getMiriamData().iterator().next();
- assertNotNull(md2);
- assertEquals(md.getDataType(), md2.getDataType());
- assertEquals(md.getRelationType(), md2.getRelationType());
- assertEquals(md.getResource(), md2.getResource());
-
- aliasDao.delete(sp);
- sp2 = (Species) aliasDao.getById(sp.getId());
- assertNull(sp2);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testProtein() throws Exception {
- try {
-
- Protein protein = new GenericProtein(testIdAlias);
- ModificationResidue mr = new ModificationResidue();
- mr.setAngle(2.0);
- mr.setName("name");
- mr.setSide("side");
- mr.setSize(3.0);
- mr.setState(ModificationState.GLYCOSYLATED);
- protein.addModificationResidue(mr);
-
- aliasDao.add(protein);
-
- Protein sp2 = (Protein) aliasDao.getById(protein.getId());
- assertNotNull(sp2);
- assertEquals(protein.getElementId(), sp2.getElementId());
-
- assertNotNull(sp2.getModificationResidues());
- assertEquals(1, sp2.getModificationResidues().size());
-
- assertEquals(sp2.getModificationResidues().get(0).getAngle(), mr.getAngle());
- assertEquals(sp2.getModificationResidues().get(0).getIdModificationResidue(), mr.getIdModificationResidue());
- assertEquals(sp2.getModificationResidues().get(0).getName(), mr.getName());
- assertEquals(sp2.getModificationResidues().get(0).getSide(), mr.getSide());
- assertEquals(sp2.getModificationResidues().get(0).getSize(), mr.getSize());
- assertEquals(sp2.getModificationResidues().get(0).getState(), mr.getState());
-
- aliasDao.delete(sp2);
- sp2 = (Protein) aliasDao.getById(protein.getId());
- assertNull(sp2);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testRna() throws Exception {
- try {
-
- Rna sp = new Rna(testIdAlias);
- RnaRegion mr = new RnaRegion();
- mr.setName("name");
- mr.setSize(3.0);
- mr.setState(ModificationState.DONT_CARE);
- sp.addRegion(mr);
-
- aliasDao.add(sp);
- aliasDao.evict(sp);
-
- Rna sp2 = (Rna) aliasDao.getById(sp.getId());
- assertNotNull(sp2);
- assertEquals(sp.getElementId(), sp2.getElementId());
-
- assertNotNull(sp2.getRegions());
- assertEquals(1, sp2.getRegions().size());
-
- assertEquals(sp2.getRegions().get(0).getId(), mr.getId());
- assertEquals(sp2.getRegions().get(0).getName(), mr.getName());
- assertEquals(sp2.getRegions().get(0).getSize(), mr.getSize(), EPSILON);
- assertEquals(sp2.getRegions().get(0).getState(), mr.getState());
-
- aliasDao.delete(sp2);
- sp2 = (Rna) aliasDao.getById(sp.getId());
- assertNull(sp2);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testAntisenseRna() throws Exception {
- try {
-
- AntisenseRna sp = new AntisenseRna(testIdAlias);
- AntisenseRnaRegion mr = new AntisenseRnaRegion();
- mr.setName("name");
- mr.setSize(3.0);
- mr.setType(AntisenseRnaRegionType.MODIFICATION_SITE);
- mr.setState(ModificationState.UNKNOWN);
- sp.addRegion(mr);
-
- aliasDao.add(sp);
- aliasDao.evict(sp);
-
- AntisenseRna sp2 = (AntisenseRna) aliasDao.getById(sp.getId());
- assertNotNull(sp2);
- assertEquals(sp.getElementId(), sp2.getElementId());
-
- assertNotNull(sp2.getRegions());
- assertEquals(1, sp2.getRegions().size());
-
- assertEquals(sp2.getRegions().get(0).getIdAntisenseRnaRegion(), mr.getIdAntisenseRnaRegion());
- assertEquals(sp2.getRegions().get(0).getName(), mr.getName());
- assertEquals(sp2.getRegions().get(0).getSize(), mr.getSize(), EPSILON);
- assertEquals(sp2.getRegions().get(0).getState(), mr.getState());
- assertEquals(sp2.getRegions().get(0).getType(), mr.getType());
-
- aliasDao.delete(sp2);
- sp2 = (AntisenseRna) aliasDao.getById(sp.getId());
- assertNull(sp2);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testSynonymsInAlias() throws Exception {
- try {
- Protein protein = new GenericProtein(testIdAlias);
- protein.addSynonym("Synonym");
- protein.addSynonym("Synonym A");
- protein.addSynonym("A");
-
- protein.addFormerSymbol("Sym");
- protein.addFormerSymbol("Sym A");
- protein.addFormerSymbol("DD");
-
- aliasDao.add(protein);
- aliasDao.flush();
-
- aliasDao.evict(protein);
- Protein sp2 = (Protein) aliasDao.getById(protein.getId());
-
- assertNotNull(sp2.getSynonyms());
- assertEquals(protein.getSynonyms().size(), sp2.getSynonyms().size());
-
- for (int i = 0; i < protein.getSynonyms().size(); i++) {
- assertEquals(protein.getSynonyms().get(i), sp2.getSynonyms().get(i));
- }
-
- assertNotNull(sp2.getFormerSymbols());
- assertEquals(protein.getFormerSymbols().size(), sp2.getFormerSymbols().size());
-
- for (int i = 0; i < protein.getFormerSymbols().size(); i++) {
- assertEquals(protein.getFormerSymbols().get(i), sp2.getFormerSymbols().get(i));
- }
-
- aliasDao.delete(sp2);
- sp2 = (Protein) aliasDao.getById(protein.getId());
- assertNull(sp2);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testChemicals() throws Exception {
- try {
- Chemical ion = new Ion(testIdAlias);
- ion.setInChI("come inchi");
- ion.setInChIKey("keyyy");
- ion.setSmiles("smile");
-
- aliasDao.add(ion);
- aliasDao.flush();
-
- aliasDao.evict(ion);
- Ion sp2 = (Ion) aliasDao.getById(ion.getId());
-
- assertNotNull(sp2.getSynonyms());
- assertEquals(ion.getSynonyms().size(), sp2.getSynonyms().size());
-
- assertEquals(ion.getSmiles(), sp2.getSmiles());
- assertEquals(ion.getInChIKey(), sp2.getInChIKey());
- assertEquals(ion.getInChI(), sp2.getInChI());
-
- aliasDao.delete(sp2);
- sp2 = (Ion) aliasDao.getById(ion.getId());
- assertNull(sp2);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testPhenotype() throws Exception {
- try {
- Phenotype phenotype = new Phenotype(testIdAlias);
-
- aliasDao.add(phenotype);
- aliasDao.flush();
-
- aliasDao.evict(phenotype);
- Phenotype sp2 = (Phenotype) aliasDao.getById(phenotype.getId());
-
- assertNotNull(sp2.getSynonyms());
- assertEquals(phenotype.getSynonyms().size(), phenotype.getSynonyms().size());
-
- aliasDao.delete(sp2);
- sp2 = (Phenotype) aliasDao.getById(phenotype.getId());
- assertNull(sp2);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
+ static Logger logger = Logger.getLogger(AliasDaoTest.class);
+
+ private Integer testChargeVal = 1;
+ private String testIdAlias = "a";
+ private Double testInitialAmount = 2.0;
+ private Double testInitialConcentration = 3.0;
+ private String testName = "d";
+ private String testNotes = "e";
+ private Boolean testOnlySubstanceunits = true;
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testAdd() throws Exception {
+ try {
+
+ GenericProtein sp = new GenericProtein(testIdAlias);
+ sp.setCharge(testChargeVal);
+ sp.setInitialAmount(testInitialAmount);
+ sp.setInitialConcentration(testInitialConcentration);
+ sp.setName(testName);
+ sp.setNotes(testNotes);
+ sp.setOnlySubstanceUnits(testOnlySubstanceunits);
+
+ Compartment parent = new Compartment("comp id");
+ sp.setCompartment(parent);
+
+ MiriamData md = new MiriamData(MiriamRelationType.BQ_BIOL_IS_DESCRIBED_BY, MiriamType.UNKNOWN, "c");
+ sp.addMiriamData(md);
+
+ aliasDao.add(sp);
+
+ Species sp2 = (Species) aliasDao.getById(sp.getId());
+ assertNotNull(sp2);
+ assertEquals(sp.getCharge(), sp2.getCharge());
+ assertEquals(sp.getElementId(), sp2.getElementId());
+ assertEquals(sp.getInitialAmount(), sp2.getInitialAmount());
+ assertEquals(sp.getInitialConcentration(), sp2.getInitialConcentration());
+ assertEquals(sp.getName(), sp2.getName());
+ assertEquals(sp.getNotes(), sp2.getNotes());
+ assertEquals(sp.hasOnlySubstanceUnits(), sp2.hasOnlySubstanceUnits());
+
+ Compartment parent2 = sp2.getCompartment();
+ assertNotNull(parent2);
+ assertEquals("comp id", parent2.getElementId());
+
+ assertNotNull(sp2.getMiriamData());
+
+ MiriamData md2 = sp2.getMiriamData().iterator().next();
+ assertNotNull(md2);
+ assertEquals(md.getDataType(), md2.getDataType());
+ assertEquals(md.getRelationType(), md2.getRelationType());
+ assertEquals(md.getResource(), md2.getResource());
+
+ aliasDao.delete(sp);
+ sp2 = (Species) aliasDao.getById(sp.getId());
+ assertNull(sp2);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testProtein() throws Exception {
+ try {
+
+ Protein protein = new GenericProtein(testIdAlias);
+ ModificationResidue mr = new ModificationResidue();
+ mr.setAngle(2.0);
+ mr.setName("name");
+ mr.setSide("side");
+ mr.setSize(3.0);
+ mr.setState(ModificationState.GLYCOSYLATED);
+ protein.addModificationResidue(mr);
+
+ aliasDao.add(protein);
+
+ Protein sp2 = (Protein) aliasDao.getById(protein.getId());
+ assertNotNull(sp2);
+ assertEquals(protein.getElementId(), sp2.getElementId());
+
+ assertNotNull(sp2.getModificationResidues());
+ assertEquals(1, sp2.getModificationResidues().size());
+
+ assertEquals(sp2.getModificationResidues().get(0).getAngle(), mr.getAngle());
+ assertEquals(sp2.getModificationResidues().get(0).getIdModificationResidue(), mr.getIdModificationResidue());
+ assertEquals(sp2.getModificationResidues().get(0).getName(), mr.getName());
+ assertEquals(sp2.getModificationResidues().get(0).getSide(), mr.getSide());
+ assertEquals(sp2.getModificationResidues().get(0).getSize(), mr.getSize());
+ assertEquals(sp2.getModificationResidues().get(0).getState(), mr.getState());
+
+ aliasDao.delete(sp2);
+ sp2 = (Protein) aliasDao.getById(protein.getId());
+ assertNull(sp2);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testRna() throws Exception {
+ try {
+
+ Rna sp = new Rna(testIdAlias);
+ RnaRegion mr = new RnaRegion();
+ mr.setName("name");
+ mr.setSize(3.0);
+ mr.setState(ModificationState.DONT_CARE);
+ sp.addRegion(mr);
+
+ aliasDao.add(sp);
+ aliasDao.evict(sp);
+
+ Rna sp2 = (Rna) aliasDao.getById(sp.getId());
+ assertNotNull(sp2);
+ assertEquals(sp.getElementId(), sp2.getElementId());
+
+ assertNotNull(sp2.getRegions());
+ assertEquals(1, sp2.getRegions().size());
+
+ assertEquals(sp2.getRegions().get(0).getId(), mr.getId());
+ assertEquals(sp2.getRegions().get(0).getName(), mr.getName());
+ assertEquals(sp2.getRegions().get(0).getSize(), mr.getSize(), EPSILON);
+ assertEquals(sp2.getRegions().get(0).getState(), mr.getState());
+
+ aliasDao.delete(sp2);
+ sp2 = (Rna) aliasDao.getById(sp.getId());
+ assertNull(sp2);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testAntisenseRna() throws Exception {
+ try {
+
+ AntisenseRna sp = new AntisenseRna(testIdAlias);
+ AntisenseRnaRegion mr = new AntisenseRnaRegion();
+ mr.setName("name");
+ mr.setSize(3.0);
+ mr.setType(AntisenseRnaRegionType.MODIFICATION_SITE);
+ mr.setState(ModificationState.UNKNOWN);
+ sp.addRegion(mr);
+
+ aliasDao.add(sp);
+ aliasDao.evict(sp);
+
+ AntisenseRna sp2 = (AntisenseRna) aliasDao.getById(sp.getId());
+ assertNotNull(sp2);
+ assertEquals(sp.getElementId(), sp2.getElementId());
+
+ assertNotNull(sp2.getRegions());
+ assertEquals(1, sp2.getRegions().size());
+
+ assertEquals(sp2.getRegions().get(0).getIdAntisenseRnaRegion(), mr.getIdAntisenseRnaRegion());
+ assertEquals(sp2.getRegions().get(0).getName(), mr.getName());
+ assertEquals(sp2.getRegions().get(0).getSize(), mr.getSize(), EPSILON);
+ assertEquals(sp2.getRegions().get(0).getState(), mr.getState());
+ assertEquals(sp2.getRegions().get(0).getType(), mr.getType());
+
+ aliasDao.delete(sp2);
+ sp2 = (AntisenseRna) aliasDao.getById(sp.getId());
+ assertNull(sp2);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testSynonymsInAlias() throws Exception {
+ try {
+ Protein protein = new GenericProtein(testIdAlias);
+ protein.addSynonym("Synonym");
+ protein.addSynonym("Synonym A");
+ protein.addSynonym("A");
+
+ protein.addFormerSymbol("Sym");
+ protein.addFormerSymbol("Sym A");
+ protein.addFormerSymbol("DD");
+
+ aliasDao.add(protein);
+ aliasDao.flush();
+
+ aliasDao.evict(protein);
+ Protein sp2 = (Protein) aliasDao.getById(protein.getId());
+
+ assertNotNull(sp2.getSynonyms());
+ assertEquals(protein.getSynonyms().size(), sp2.getSynonyms().size());
+
+ for (int i = 0; i < protein.getSynonyms().size(); i++) {
+ assertEquals(protein.getSynonyms().get(i), sp2.getSynonyms().get(i));
+ }
+
+ assertNotNull(sp2.getFormerSymbols());
+ assertEquals(protein.getFormerSymbols().size(), sp2.getFormerSymbols().size());
+
+ for (int i = 0; i < protein.getFormerSymbols().size(); i++) {
+ assertEquals(protein.getFormerSymbols().get(i), sp2.getFormerSymbols().get(i));
+ }
+
+ aliasDao.delete(sp2);
+ sp2 = (Protein) aliasDao.getById(protein.getId());
+ assertNull(sp2);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testChemicals() throws Exception {
+ try {
+ Chemical ion = new Ion(testIdAlias);
+ ion.setInChI("come inchi");
+ ion.setInChIKey("keyyy");
+ ion.setSmiles("smile");
+
+ aliasDao.add(ion);
+ aliasDao.flush();
+
+ aliasDao.evict(ion);
+ Ion sp2 = (Ion) aliasDao.getById(ion.getId());
+
+ assertNotNull(sp2.getSynonyms());
+ assertEquals(ion.getSynonyms().size(), sp2.getSynonyms().size());
+
+ assertEquals(ion.getSmiles(), sp2.getSmiles());
+ assertEquals(ion.getInChIKey(), sp2.getInChIKey());
+ assertEquals(ion.getInChI(), sp2.getInChI());
+
+ aliasDao.delete(sp2);
+ sp2 = (Ion) aliasDao.getById(ion.getId());
+ assertNull(sp2);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testPhenotype() throws Exception {
+ try {
+ Phenotype phenotype = new Phenotype(testIdAlias);
+
+ aliasDao.add(phenotype);
+ aliasDao.flush();
+
+ aliasDao.evict(phenotype);
+ Phenotype sp2 = (Phenotype) aliasDao.getById(phenotype.getId());
+
+ assertNotNull(sp2.getSynonyms());
+ assertEquals(phenotype.getSynonyms().size(), phenotype.getSynonyms().size());
+
+ aliasDao.delete(sp2);
+ sp2 = (Phenotype) aliasDao.getById(phenotype.getId());
+ assertNull(sp2);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
}
diff --git a/service/src/main/java/lcsb/mapviewer/services/search/data/FullAliasView.java b/service/src/main/java/lcsb/mapviewer/services/search/data/FullAliasView.java
index 3fdec74966cd3d723b2b40340ada9cd3328cb9d2..587ba905d8508e604613c718b66b25188047f624 100644
--- a/service/src/main/java/lcsb/mapviewer/services/search/data/FullAliasView.java
+++ b/service/src/main/java/lcsb/mapviewer/services/search/data/FullAliasView.java
@@ -22,611 +22,611 @@ import lcsb.mapviewer.services.view.AnnotationView;
*/
public class FullAliasView extends LightAliasView implements IHeavyView {
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private static Logger logger = Logger.getLogger(FullAliasView.class);
-
- /**
- * This class represents posttransational modification of the element.
- *
- * @author Piotr Gawron
- *
- */
- public static class PosttransationalModification implements Serializable {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Name of the modification.
- */
- private String name;
-
- /**
- * Position where the modification occurred.
- */
- private String position;
-
- /**
- * @return the name
- * @see #name
- */
- public String getName() {
- return name;
- }
-
- /**
- * @param name
- * the name to set
- * @see #name
- */
- public void setName(String name) {
- this.name = name;
- }
-
- /**
- * @return the position
- * @see #position
- */
- public String getPosition() {
- return position;
- }
-
- /**
- * @param position
- * the position to set
- * @see #position
- */
- public void setPosition(String position) {
- this.position = position;
- }
- }
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Description.
- *
- * @see Element#notes
- */
- private String notes;
-
- /**
- * Type of the alias.
- *
- * @see Element#getStringType()
- */
- private String type;
-
- /**
- * Symbol of the element.
- *
- * @see Element#symbol
- */
- private String symbol;
-
- /**
- * Full name of the element.
- *
- * @see Element#fullName
- */
- private String fullName;
-
- /**
- * Abbreviation of the element.
- *
- * @see Element#abbreviation
- */
- private String abbreviation;
-
- /**
- * Formula describing the element.
- *
- * @see Element#formula
- */
- private String formula;
-
- /**
- * Charge of the element.
- *
- * @see Species#charge
- */
- private Integer charge;
-
- /**
- * Initial amount of species.
- *
- * @see Species#initialAmount
- */
- private Integer initialAmount = null;
-
- private String visibilityLevel = null;
-
- /**
- * Initial concentration of species.
- *
- * @see Species#initialConcentration
- */
- private Integer initialConcentration = null;
-
- /**
- * Is only substance units allowed in a species.
- *
- * @see Species#onlySubstanceUnits
- */
- private Boolean onlySubstanceUnits = null;
-
- /**
- * Name of the element.
- *
- * @see Element#name
- */
- private String name = "";
-
- /**
- * Name of the {@link Element#model}.
- */
- private String modelName;
-
- /**
- * Name of the {@link Element#submodel}.
- */
- private String submodelName;
-
- /**
- * Id of the {@link Element#submodel}.
- */
- private String submodelId;
-
- /**
- * List of synonyms of the element.
- *
- * @see Element#synonyms
- */
- private List<String> synonyms = new ArrayList<>();
-
- /**
- * List of former symbols used by the entity represented by this element.
- *
- * @see Element#formerSymbols
- */
- private List<String> formerSymbols = new ArrayList<>();
-
- /**
- * List of references for this element.
- *
- * @see Element#miriamData
- */
- private List<AnnotationView> references = new ArrayList<>();
-
- /**
- * List of other unstructurized feuters, specific for some subclases of Alias.
- *
- */
- private Map<String, Object> other = new HashMap<>();
-
- /**
- * Default constructor.
- *
- * @param element
- * original object from which this element is created
- * @param icon
- * string with icon that should be used to visualize this alias
- */
- protected FullAliasView(Element element, String icon) {
- super(element, icon);
- setModelName(element.getModel().getName());
- if (element != null) {
- setAbbreviation(element.getAbbreviation());
- addFormerSymbols(element.getFormerSymbols());
- setFormula(element.getFormula());
- setFullName(element.getFullName());
- setName(element.getName());
- setNotes(element.getNotes());
- setSymbol(element.getSymbol());
- addSynonyms(element.getSynonyms());
- setType(element.getStringType());
- setVisibilityLevel(element.getVisibilityLevel());
- if (element instanceof Species) {
- Species species = (Species) element;
- setCharge(species.getCharge());
- setInitialAmount(species.getInitialAmount());
- setInitialConcentration(species.getInitialConcentration());
- setOnlySubstanceUnits(species.getOnlySubstanceUnits());
- if (element.getSubmodel() != null && element.getSubmodel().getSubmodel() != null) {
- setSubmodelName(element.getSubmodel().getSubmodel().getName());
- setSubmodelId(element.getSubmodel().getSubmodel().getId() + "");
- }
- }
- }
- }
-
- /**
- * Constructor that should be used only by the deserialization method.
- */
- protected FullAliasView() {
- }
-
- /**
- * Adds elements to {@link #synonyms} list.
- *
- * @param synonyms2
- * list of elements to add
- */
- private void addSynonyms(List<String> synonyms2) {
- synonyms.addAll(synonyms2);
- }
-
- /**
- * Adds elements to {@link #formerSymbols} list.
- *
- * @param formerSymbols2
- * list of elements to add
- */
- private void addFormerSymbols(List<String> formerSymbols2) {
- formerSymbols.addAll(formerSymbols2);
- }
-
- /**
- * @return the notes
- * @see #notes
- */
- public String getNotes() {
- return notes;
- }
-
- /**
- * @param notes
- * the notes to set
- * @see #notes
- */
- public void setNotes(String notes) {
- this.notes = notes;
- }
-
- /**
- * @return the symbol
- * @see #symbol
- */
- public String getSymbol() {
- return symbol;
- }
-
- /**
- * @param symbol
- * the symbol to set
- * @see #symbol
- */
- public void setSymbol(String symbol) {
- this.symbol = symbol;
- }
-
- /**
- * @return the fullName
- * @see #fullName
- */
- public String getFullName() {
- return fullName;
- }
-
- /**
- * @param fullName
- * the fullName to set
- * @see #fullName
- */
- public void setFullName(String fullName) {
- this.fullName = fullName;
- }
-
- /**
- * @return the abbreviation
- * @see #abbreviation
- */
- public String getAbbreviation() {
- return abbreviation;
- }
-
- /**
- * @param abbreviation
- * the abbreviation to set
- * @see #abbreviation
- */
- public void setAbbreviation(String abbreviation) {
- this.abbreviation = abbreviation;
- }
-
- /**
- * @return the formula
- * @see #formula
- */
- public String getFormula() {
- return formula;
- }
-
- /**
- * @param formula
- * the formula to set
- * @see #formula
- */
- public void setFormula(String formula) {
- this.formula = formula;
- }
-
- /**
- * @return the name
- * @see #name
- */
- public String getName() {
- return name;
- }
-
- /**
- * @param name
- * the name to set
- * @see #name
- */
- public void setName(String name) {
- this.name = name;
- }
-
- /**
- * @return the synonyms
- * @see #synonyms
- */
- public List<String> getSynonyms() {
- return synonyms;
- }
-
- /**
- * @param synonyms
- * the synonyms to set
- * @see #synonyms
- */
- public void setSynonyms(List<String> synonyms) {
- this.synonyms = synonyms;
- }
-
- /**
- * @return the formerSymbols
- * @see #formerSymbols
- */
- public List<String> getFormerSymbols() {
- return formerSymbols;
- }
-
- /**
- * @param formerSymbols
- * the formerSymbols to set
- * @see #formerSymbols
- */
- public void setFormerSymbols(List<String> formerSymbols) {
- this.formerSymbols = formerSymbols;
- }
-
- /**
- * @return the references
- * @see #references
- */
- public List<AnnotationView> getReferences() {
- return references;
- }
-
- /**
- * @param references
- * the references to set
- * @see #references
- */
- public void setReferences(List<AnnotationView> references) {
- this.references = references;
- }
-
- /**
- * @return the other
- * @see #other
- */
- public Map<String, Object> getOther() {
- return other;
- }
-
- /**
- * Returns other (additional element) by the name.
- *
- * @param key
- * key identifing the feature.
- * @return other (additional element) by the name
- */
- public Object getOther(String key) {
- return other.get(key);
- }
-
- /**
- * @param other
- * the other to set
- * @see #other
- */
- public void setOther(Map<String, Object> other) {
- this.other = other;
- }
-
- /**
- * @return the type
- * @see #type
- */
- public String getType() {
- return type;
- }
-
- /**
- * @param type
- * the type to set
- * @see #type
- */
- public void setType(String type) {
- this.type = type;
- }
-
- /**
- * Adds elements to {@link #references} list.
- *
- * @param newReferences
- * list of elements to add
- */
- public void addReferences(List<AnnotationView> newReferences) {
- references.addAll(newReferences);
- }
-
- /**
- * Addsother (additional element) by the name.
- *
- * @param key
- * name of the feature
- * @param value
- * object representing data of the feature
- */
- public void addOther(String key, Object value) {
- other.put(key, value);
- }
-
- /**
- * @return the modelName
- * @see #modelName
- */
- public String getModelName() {
- return modelName;
- }
-
- /**
- * @param modelName
- * the modelName to set
- * @see #modelName
- */
- public void setModelName(String modelName) {
- this.modelName = modelName;
- }
-
- /**
- * @return the charge
- * @see #charge
- */
- public Integer getCharge() {
- return charge;
- }
-
- /**
- * @param charge
- * the charge to set
- * @see #charge
- */
- public void setCharge(Integer charge) {
- this.charge = charge;
- }
-
- /**
- * @return the initialAmount
- * @see #initialAmount
- */
- public Integer getInitialAmount() {
- return initialAmount;
- }
-
- /**
- * @param initialAmount
- * the initialAmount to set
- * @see #initialAmount
- */
- public void setInitialAmount(Integer initialAmount) {
- this.initialAmount = initialAmount;
- }
-
- /**
- * @return the initialConcentration
- * @see #initialConcentration
- */
- public Integer getInitialConcentration() {
- return initialConcentration;
- }
-
- /**
- * @param initialConcentration
- * the initialConcentration to set
- * @see #initialConcentration
- */
- public void setInitialConcentration(Integer initialConcentration) {
- this.initialConcentration = initialConcentration;
- }
-
- /**
- * @return the onlySubstanceUnits
- * @see #onlySubstanceUnits
- */
- public Boolean getOnlySubstanceUnits() {
- return onlySubstanceUnits;
- }
-
- /**
- * @param onlySubstanceUnits
- * the onlySubstanceUnits to set
- * @see #onlySubstanceUnits
- */
- public void setOnlySubstanceUnits(Boolean onlySubstanceUnits) {
- this.onlySubstanceUnits = onlySubstanceUnits;
- }
-
- /**
- * @return the submodelName
- * @see #submodelName
- */
- public String getSubmodelName() {
- return submodelName;
- }
-
- /**
- * @param submodelName
- * the submodelName to set
- * @see #submodelName
- */
- public void setSubmodelName(String submodelName) {
- this.submodelName = submodelName;
- }
-
- /**
- * @return the submodelId
- * @see #submodelId
- */
- public String getSubmodelId() {
- return submodelId;
- }
-
- /**
- * @param submodelId
- * the submodelId to set
- * @see #submodelId
- */
- public void setSubmodelId(String submodelId) {
- this.submodelId = submodelId;
- }
-
- /**
- * @return the visibilityLevel
- * @see #visibilityLevel
- */
- public String getVisibilityLevel() {
- return visibilityLevel;
- }
-
- /**
- * @param visibilityLevel
- * the visibilityLevel to set
- * @see #visibilityLevel
- */
- public void setVisibilityLevel(String visibilityLevel) {
- this.visibilityLevel = visibilityLevel;
- }
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private static Logger logger = Logger.getLogger(FullAliasView.class);
+
+ /**
+ * This class represents posttransational modification of the element.
+ *
+ * @author Piotr Gawron
+ *
+ */
+ public static class PosttransationalModification implements Serializable {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Name of the modification.
+ */
+ private String name;
+
+ /**
+ * Position where the modification occurred.
+ */
+ private String position;
+
+ /**
+ * @return the name
+ * @see #name
+ */
+ public String getName() {
+ return name;
+ }
+
+ /**
+ * @param name
+ * the name to set
+ * @see #name
+ */
+ public void setName(String name) {
+ this.name = name;
+ }
+
+ /**
+ * @return the position
+ * @see #position
+ */
+ public String getPosition() {
+ return position;
+ }
+
+ /**
+ * @param position
+ * the position to set
+ * @see #position
+ */
+ public void setPosition(String position) {
+ this.position = position;
+ }
+ }
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Description.
+ *
+ * @see Element#notes
+ */
+ private String notes;
+
+ /**
+ * Type of the alias.
+ *
+ * @see Element#getStringType()
+ */
+ private String type;
+
+ /**
+ * Symbol of the element.
+ *
+ * @see Element#symbol
+ */
+ private String symbol;
+
+ /**
+ * Full name of the element.
+ *
+ * @see Element#fullName
+ */
+ private String fullName;
+
+ /**
+ * Abbreviation of the element.
+ *
+ * @see Element#abbreviation
+ */
+ private String abbreviation;
+
+ /**
+ * Formula describing the element.
+ *
+ * @see Element#formula
+ */
+ private String formula;
+
+ /**
+ * Charge of the element.
+ *
+ * @see Species#charge
+ */
+ private Integer charge;
+
+ /**
+ * Initial amount of species.
+ *
+ * @see Species#initialAmount
+ */
+ private Double initialAmount = null;
+
+ private String visibilityLevel = null;
+
+ /**
+ * Initial concentration of species.
+ *
+ * @see Species#initialConcentration
+ */
+ private Double initialConcentration = null;
+
+ /**
+ * Is only substance units allowed in a species.
+ *
+ * @see Species#onlySubstanceUnits
+ */
+ private Boolean onlySubstanceUnits = null;
+
+ /**
+ * Name of the element.
+ *
+ * @see Element#name
+ */
+ private String name = "";
+
+ /**
+ * Name of the {@link Element#model}.
+ */
+ private String modelName;
+
+ /**
+ * Name of the {@link Element#submodel}.
+ */
+ private String submodelName;
+
+ /**
+ * Id of the {@link Element#submodel}.
+ */
+ private String submodelId;
+
+ /**
+ * List of synonyms of the element.
+ *
+ * @see Element#synonyms
+ */
+ private List<String> synonyms = new ArrayList<>();
+
+ /**
+ * List of former symbols used by the entity represented by this element.
+ *
+ * @see Element#formerSymbols
+ */
+ private List<String> formerSymbols = new ArrayList<>();
+
+ /**
+ * List of references for this element.
+ *
+ * @see Element#miriamData
+ */
+ private List<AnnotationView> references = new ArrayList<>();
+
+ /**
+ * List of other unstructurized feuters, specific for some subclases of Alias.
+ *
+ */
+ private Map<String, Object> other = new HashMap<>();
+
+ /**
+ * Default constructor.
+ *
+ * @param element
+ * original object from which this element is created
+ * @param icon
+ * string with icon that should be used to visualize this alias
+ */
+ protected FullAliasView(Element element, String icon) {
+ super(element, icon);
+ setModelName(element.getModel().getName());
+ if (element != null) {
+ setAbbreviation(element.getAbbreviation());
+ addFormerSymbols(element.getFormerSymbols());
+ setFormula(element.getFormula());
+ setFullName(element.getFullName());
+ setName(element.getName());
+ setNotes(element.getNotes());
+ setSymbol(element.getSymbol());
+ addSynonyms(element.getSynonyms());
+ setType(element.getStringType());
+ setVisibilityLevel(element.getVisibilityLevel());
+ if (element instanceof Species) {
+ Species species = (Species) element;
+ setCharge(species.getCharge());
+ setInitialAmount(species.getInitialAmount());
+ setInitialConcentration(species.getInitialConcentration());
+ setOnlySubstanceUnits(species.getOnlySubstanceUnits());
+ if (element.getSubmodel() != null && element.getSubmodel().getSubmodel() != null) {
+ setSubmodelName(element.getSubmodel().getSubmodel().getName());
+ setSubmodelId(element.getSubmodel().getSubmodel().getId() + "");
+ }
+ }
+ }
+ }
+
+ /**
+ * Constructor that should be used only by the deserialization method.
+ */
+ protected FullAliasView() {
+ }
+
+ /**
+ * Adds elements to {@link #synonyms} list.
+ *
+ * @param synonyms2
+ * list of elements to add
+ */
+ private void addSynonyms(List<String> synonyms2) {
+ synonyms.addAll(synonyms2);
+ }
+
+ /**
+ * Adds elements to {@link #formerSymbols} list.
+ *
+ * @param formerSymbols2
+ * list of elements to add
+ */
+ private void addFormerSymbols(List<String> formerSymbols2) {
+ formerSymbols.addAll(formerSymbols2);
+ }
+
+ /**
+ * @return the notes
+ * @see #notes
+ */
+ public String getNotes() {
+ return notes;
+ }
+
+ /**
+ * @param notes
+ * the notes to set
+ * @see #notes
+ */
+ public void setNotes(String notes) {
+ this.notes = notes;
+ }
+
+ /**
+ * @return the symbol
+ * @see #symbol
+ */
+ public String getSymbol() {
+ return symbol;
+ }
+
+ /**
+ * @param symbol
+ * the symbol to set
+ * @see #symbol
+ */
+ public void setSymbol(String symbol) {
+ this.symbol = symbol;
+ }
+
+ /**
+ * @return the fullName
+ * @see #fullName
+ */
+ public String getFullName() {
+ return fullName;
+ }
+
+ /**
+ * @param fullName
+ * the fullName to set
+ * @see #fullName
+ */
+ public void setFullName(String fullName) {
+ this.fullName = fullName;
+ }
+
+ /**
+ * @return the abbreviation
+ * @see #abbreviation
+ */
+ public String getAbbreviation() {
+ return abbreviation;
+ }
+
+ /**
+ * @param abbreviation
+ * the abbreviation to set
+ * @see #abbreviation
+ */
+ public void setAbbreviation(String abbreviation) {
+ this.abbreviation = abbreviation;
+ }
+
+ /**
+ * @return the formula
+ * @see #formula
+ */
+ public String getFormula() {
+ return formula;
+ }
+
+ /**
+ * @param formula
+ * the formula to set
+ * @see #formula
+ */
+ public void setFormula(String formula) {
+ this.formula = formula;
+ }
+
+ /**
+ * @return the name
+ * @see #name
+ */
+ public String getName() {
+ return name;
+ }
+
+ /**
+ * @param name
+ * the name to set
+ * @see #name
+ */
+ public void setName(String name) {
+ this.name = name;
+ }
+
+ /**
+ * @return the synonyms
+ * @see #synonyms
+ */
+ public List<String> getSynonyms() {
+ return synonyms;
+ }
+
+ /**
+ * @param synonyms
+ * the synonyms to set
+ * @see #synonyms
+ */
+ public void setSynonyms(List<String> synonyms) {
+ this.synonyms = synonyms;
+ }
+
+ /**
+ * @return the formerSymbols
+ * @see #formerSymbols
+ */
+ public List<String> getFormerSymbols() {
+ return formerSymbols;
+ }
+
+ /**
+ * @param formerSymbols
+ * the formerSymbols to set
+ * @see #formerSymbols
+ */
+ public void setFormerSymbols(List<String> formerSymbols) {
+ this.formerSymbols = formerSymbols;
+ }
+
+ /**
+ * @return the references
+ * @see #references
+ */
+ public List<AnnotationView> getReferences() {
+ return references;
+ }
+
+ /**
+ * @param references
+ * the references to set
+ * @see #references
+ */
+ public void setReferences(List<AnnotationView> references) {
+ this.references = references;
+ }
+
+ /**
+ * @return the other
+ * @see #other
+ */
+ public Map<String, Object> getOther() {
+ return other;
+ }
+
+ /**
+ * Returns other (additional element) by the name.
+ *
+ * @param key
+ * key identifing the feature.
+ * @return other (additional element) by the name
+ */
+ public Object getOther(String key) {
+ return other.get(key);
+ }
+
+ /**
+ * @param other
+ * the other to set
+ * @see #other
+ */
+ public void setOther(Map<String, Object> other) {
+ this.other = other;
+ }
+
+ /**
+ * @return the type
+ * @see #type
+ */
+ public String getType() {
+ return type;
+ }
+
+ /**
+ * @param type
+ * the type to set
+ * @see #type
+ */
+ public void setType(String type) {
+ this.type = type;
+ }
+
+ /**
+ * Adds elements to {@link #references} list.
+ *
+ * @param newReferences
+ * list of elements to add
+ */
+ public void addReferences(List<AnnotationView> newReferences) {
+ references.addAll(newReferences);
+ }
+
+ /**
+ * Addsother (additional element) by the name.
+ *
+ * @param key
+ * name of the feature
+ * @param value
+ * object representing data of the feature
+ */
+ public void addOther(String key, Object value) {
+ other.put(key, value);
+ }
+
+ /**
+ * @return the modelName
+ * @see #modelName
+ */
+ public String getModelName() {
+ return modelName;
+ }
+
+ /**
+ * @param modelName
+ * the modelName to set
+ * @see #modelName
+ */
+ public void setModelName(String modelName) {
+ this.modelName = modelName;
+ }
+
+ /**
+ * @return the charge
+ * @see #charge
+ */
+ public Integer getCharge() {
+ return charge;
+ }
+
+ /**
+ * @param charge
+ * the charge to set
+ * @see #charge
+ */
+ public void setCharge(Integer charge) {
+ this.charge = charge;
+ }
+
+ /**
+ * @return the initialAmount
+ * @see #initialAmount
+ */
+ public Double getInitialAmount() {
+ return initialAmount;
+ }
+
+ /**
+ * @param initialAmount
+ * the initialAmount to set
+ * @see #initialAmount
+ */
+ public void setInitialAmount(Double initialAmount) {
+ this.initialAmount = initialAmount;
+ }
+
+ /**
+ * @return the initialConcentration
+ * @see #initialConcentration
+ */
+ public Double getInitialConcentration() {
+ return initialConcentration;
+ }
+
+ /**
+ * @param initialConcentration
+ * the initialConcentration to set
+ * @see #initialConcentration
+ */
+ public void setInitialConcentration(Double initialConcentration) {
+ this.initialConcentration = initialConcentration;
+ }
+
+ /**
+ * @return the onlySubstanceUnits
+ * @see #onlySubstanceUnits
+ */
+ public Boolean getOnlySubstanceUnits() {
+ return onlySubstanceUnits;
+ }
+
+ /**
+ * @param onlySubstanceUnits
+ * the onlySubstanceUnits to set
+ * @see #onlySubstanceUnits
+ */
+ public void setOnlySubstanceUnits(Boolean onlySubstanceUnits) {
+ this.onlySubstanceUnits = onlySubstanceUnits;
+ }
+
+ /**
+ * @return the submodelName
+ * @see #submodelName
+ */
+ public String getSubmodelName() {
+ return submodelName;
+ }
+
+ /**
+ * @param submodelName
+ * the submodelName to set
+ * @see #submodelName
+ */
+ public void setSubmodelName(String submodelName) {
+ this.submodelName = submodelName;
+ }
+
+ /**
+ * @return the submodelId
+ * @see #submodelId
+ */
+ public String getSubmodelId() {
+ return submodelId;
+ }
+
+ /**
+ * @param submodelId
+ * the submodelId to set
+ * @see #submodelId
+ */
+ public void setSubmodelId(String submodelId) {
+ this.submodelId = submodelId;
+ }
+
+ /**
+ * @return the visibilityLevel
+ * @see #visibilityLevel
+ */
+ public String getVisibilityLevel() {
+ return visibilityLevel;
+ }
+
+ /**
+ * @param visibilityLevel
+ * the visibilityLevel to set
+ * @see #visibilityLevel
+ */
+ public void setVisibilityLevel(String visibilityLevel) {
+ this.visibilityLevel = visibilityLevel;
+ }
}